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Those little cells either self discharge quickly and/or the standby draw from these little lights is enough to exhaust the battery fairly quickly. I have the same behavior with mine, I just leave it partially unscrewed and that mostly takes care of the issue. This light is really a novelty to me but I have a couple and I found a aaa size tube that works for it. I’m using a 10440 with great success as a daily carry.
For somebody that’s afraid of lithium-ion batteries you certainly are asking for trouble. Do you run your car out of gas before you put more in? Do you run your tires down until you see the steel belt showing?
So you don’t understand what you’re doing, and you figure you can ignore warning lights/signals. It’s a tiny little cell. Read up about voltage sag.
CRC… No biggie, just get you a volt meter (cheap is OK for this use) & check the voltage of battery in question.
Then go from there. 
You’re asking question & learning, keep it up.
I would suppose you're fine, but the best thing would be to get a multimeter and check them just to be sure. I don't have that light or any cells that size, but I can't imagine they would have discharged that much further. When a battery is in use/draining and then you stop the drain, it will nearly always rebound a little bit. So, if you pull the battery at 3v when the light blinks to you, you may find that in a few minutes the cell has rebounded back up to 3.1v or something. Totally normal. Now, if the light is accurate and 3v is the blink, and then you leave it and there is some parasitic drain or something...then it continues to discharge a little, right? Probably only a small amount but what you may be seeing is the actual voltage cutoff in the light rather than the voltage warning. Warning gives you notice, cutoff shuts it down for protection. Maybe that's 2.8v or something (typical).
Even the cheapest cheap-o multimeters for $5 or whatever would be fine for this, so pick one up when you can...super simple to use and no risk when checking a battery. In the meantime, put it on the charger and just keep an eye on it. If it's getting very warm/hot, there may be a problem with it (i.e. warmer than it normally did before...some warmth is normal).
Keeping a cell discharged for a length of time is not good for its health (it may lose some capacity or cycle life) but it's generally not dangerous unless you're talking severely overdischarged where they're down at 2v or less for awhile. But...respect...so proceed and keep an eye on it...and get a multimeter when you can do so. (actually for the most part if you have a good smart charger that shows voltage that's almost good enough here...you can throw the battery in there and just see what it tells you...can always yank it back out before charging progresses if you want to. The advantage of the multimeter is that it will be a truth teller just in case the circuitry in the flashlight or the charger is not accurate/not the same.)
If it helps you relax any, the laboratory testing for many cells shows discharging (at a low rate) down to like 2.7v or sometimes 2.5v...this is usually how a cell's full capacity is measured by the manufacturers. They do that a lot in testing, and while we try not to go that low just for the sake of the cell's longevity/life cycles, it's not terribly harmful when it's for a brief period even if it sits for a bit before recharging. And remember, modern lithium-ion chemistries are much better than older ones, and different than the lithium-metal primary cells (like the CR123)...and generally using only one rather than two in series which complicates things. Pretty safe here, and when drivers have protection modes built in, it's much harder to get stupid or dangerous.
Should add that not all lights have both the low voltage warning and the low voltage cutoff...some only have one or the other. I didn't follow the development or reviews for this light so I don't know for sure. But also, some lights just won't light up at all if the voltage is so low that it can't push its way through the electronics to give enough juice. Generally 3v emitters are what we use the most, but depending on which specific "bin" they are they may light up as low as 2.5v or only 2.8v. The other electronic components will shave a little of the battery voltage away, so it's possible that if a cell is low and the light doesn't have a cutoff mode, the light still may refuse to light up (like self protection, sorta...haha). Hope this isn't confusing or too much info...just trying to explain the low end of run time if it helps you understand and feel safer.
Or put this way...it's hard to say whether your track and field runner is just pooped out after a meet or if the coach is sidelining him, but he's likely just fine either way. Doctor visit would be best but give him an energy drink and see how he feels...probably ready to race again.
I quarter turn my tail cap on all lights with electronic switch . Including GT Nano. This has horrendous drain.
A friend of a friend had a GT nano that discharged all the way down to 2v. He put it in his charger anyway and charged it all the way back up and put it back into his flashlight. That night while he was sleeping it exploded and leveled that entire end of his house. Luckily it was a ranch house and his bedroom was on the other end or he probably would have died and been blown to bits. I shudder to think just how bad it could have been.
Just kidding, you’ll probably be fine. If not, we’ll miss you here.
For crystals and such...you don't/can't really, other than some of the signs such as increased resistance or abnormal heat in operation/charging. Your cells didn't go down far enough or stay there for you to be very concerned about this, truthfully. And I may be wrong about this but I think the potential damage was a little higher with older early lithium-ion chemistries than what we use today mostly.
I'll be the last guy to tell you have have to spend money, but I took a quick look at some Canada prices for cheapie meters. Amazon surely offers more than Canadian Tire (didn't see a better offer at the latter, so just amazon links here).
This looks like it can be $13.99 right now and it's fine. There are places the cheapies fall short or just aren't adequate but for basic voltage and many other measurements, they're ok.
https://www.amazon.ca/Zacro-Digital-Multimeter-Voltmeter-Ohmmeter/dp/B06XC5QFS9/
Now this one...and I am trying to remember the differences in USD vs CAD when I look at numbers...is kind of over the top ridiculously priced, but it's an example. Neiko is just a Chinese re-badger of products with a heavy marketing angle...and this meter is a fine example. This design is ubiquitous and has been around in exactly the same form for at least 25 years that I'm aware of, starting with the early "Cal-Tech" imports in the early 90s. They don't seem any better or worse than they ever did...which is kind of amazing. Here in the US you see these - in various colors - selling in the bargain stores for like $5 or $7, sometimes overpriced at $10...and I've seen them given away as freebies with a purchase or for $3 with a coupon discount. You might be able to see more on your Amazon than I do and maybe someone has this same meter for a lot less money...worth a look maybe. I'm sure you could order one of these on aliexpress for a couple bucks, too, from any of a thousand sellers. Have to be careful with the shoddy leads on these units and they are not well made at all, but accurate enough for basic voltage and can last a long time if you don't abuse them. The price here of $20 is crazy, though. There are a ton of much better meters in that price range, so this is just for a visual example of what can be had for usually super cheap prices. I suppose you guys have "dollar stores" up there, too, and sometimes those will stock a meter like this (probably even walmart). https://www.amazon.ca/Neiko-40508-Hand-Held-Multimeter-Transistor/dp/B00066ZZO4/
And remember that all of the above advice and these basic procedures and stuff are just best-practice. Learn it, try to do it when you're able to get the equipment, but don't sweat it right now. You understand and are doing what you should in regard to overdischarge...that's great. Keep in mind that "over" generally means really drained down loooowww, though, like in a neglected battery pack or a big oops with a flashlight that doesn't have any protection circuitry at all. For the lab tests/datasheets, cells are typically drained to where yours were at or sometimes lower, and that's ok when you juice 'em up afterwards, just best not to make a habit of it so that you can get longer run times and more charge cycles over the life of the cell.
Lol, got mine 20 years ago from Dick Smiths iirc in Australia
Keep in mind that the little beastie is a keychain light, one step above a toy. (Watch me get dogpiled on…)
A 10180 wouldn’t even power an AAA light beyond a few minutes at any appreciable brightness, and from I saw from The Flasholic’s review, “turbo” lasts a whopping 3.2sec before flashing “no mas!”. So you might as well keep it tethered to a cable and powerbank.
So it’s kewl af to show off… quickly… then sneak it back into your pocket. But running it down repeatedly ain’t doing that 10180 any favors.
Best is to just top it off after using it, well, at all. Who knows how many minutes at any random brightness uses up so-and-so much juice.
Actual, measured runtimes: (No, I don’t remember the website from a year ago…)
525L-2 minutes
150L - 21 minutes
1L - 16 HOURS
It’s certainly capable of real-world usage, assuming the operator isn’t dumber than, well-you know.
Lumintop sell the 10440 tubes for about $5 so I’ve just had one arrive in the post. Finding a trustworthy 10440 here in the U.K. is another matter, but it’s the way forward for this little light.
I left mine for a while without cracking the tail cap and also have a dead cell, there is quite a drain.
10180 = Garbage from day one. Will not buy any flashlight that can only use this abomination of a cell.
Fortunately this flashlight can use a variety of battery tubes from various other brands that use the much better 10440 battery.
Then it is a legit backup/showoff EDC.
Peace out,
Keith