Yes, this is most likely what happened. It makes sense: Enemy reacted to TearGas by retreating and closing the door. Then probably there is no cloud check for indoors if the epicenter of TearGas is outside and doors are closed (with the intention that it cannot enter closed building, but in this case it had already came in).

Great, then i tihnk its possible to be fixed (not perfectly, but still), despite its really rare case.

Afterthought im not sure now its worthy to bother tho. This bug require really rare prerequisites to happens, and effect in 3 known to me effects, all of them seems to be minor:
1. It will stop gas cloud cut by a door from its epicenter from applying breath damage, spreading, or disappearing in time (actually door is not of something special here, just its only known to me object that could disappear and reappear on already loaded map during normal gameplay).
2. It will affect AI movement decisions, as AI set to evade tiles with gas, even if that gas actually have no effect due to bug.
3. It will produce a visual glitch for player, as the cloud area shown is actually of no real effect to player's mercs.

2&3 are merely consequences of 1, and only they could be relatively easily fixed, while 1 would require a complex rewrite of mechanic itself. But fix for 2&3 is still not that easy for its effect and chance of happening. Im not guarantee it then.

I have also had other visual glitch. I made a screenshot, it is not preserved in a save. A minor bug, leftovers from the animation of killing snake with a knife are still visible. I think other animations can cause similar problems.

Unrelated question: does kneeling increase the chance to be hit in head or it just reduces chances to be hit?

Does its goes away after change a screen, say, opening Inventory or Map? If yes, then id say its not a problem. I did seen many other similar visual artifacts, yes, usually with some item's image leftovers. Thats the way they draw stuff: preserve a screen's content sometimes, then reload it, and in some cases it would keep old unrelated parts of picture not cleared. If its not goes away on redraw of the screen is a problem tho.

Its only reduce chances to be hit with bullet, thats all. Unlike it, prone position (include swimming), make chance to hit with bullet additionally lower; it require bullet to fly low indeed to hit a merc. But even in case of hit in prone, distrubution of hit areas remain the same. As i understand they improved that mechanic in JA2, here its very rudimentary.

Another type of lockup, unfortunately:
https://www.dropbox.com/s/ol1uswqut7flkk0/QUICK.SAV?dl=0
Game froze on opponent's turn, some options still working, including alt-x, hence the save.
One special event preceded it: Smoke got hit, losing points of agility (you can still see the effect by pressing "s") - maybe this is related to the freeze?

UPDATE: I left the game running on this save for a long time, like 10 minutes, and when I got back, I found it miraculously unfreezed, all normal.

What I meant was it got back to normal. I also have noticed that if you abort and restart the day the game is still freezed for some time.

Its critical hit to leg while crouched indeed there. Such hit should also drop a person who received it to ground, but that part didnt worked for crouch, so it sorta freeze. Its not good to tie animations to game mechanics, again. Tho this freeze not full indeed, and game recover eventually, probably it possible to be speeded up a bit for similar cases. Thats amazing how you manage to keep getting those oddities on, really thanks for it, man.

This one is more obvious: strictly speaking Abort function should be possible only in player's turn, otherwise it act described way, spend a whole turn without passing full commands to player. I just didnt bother to fix it in past, as its not really break anything, and player can compress time and abort again without persisting problem anymore. And if fixed it would mean that player would have to wait a whole Enemy turn to be able to abort. And good fix of it will take more efforts than bother it causing.

One more older save: https://www.dropbox.com/s/ol1uswqut7flkk0/QUICK.SAV?dl=0
Hurl has been ordered to give first aid, but only the animation is actually triggered. No first aid is given and Snake can walk away leaving Hurl bandaging air. The only distinct circumstance I remember is that Hurl was stopped giving first aid (to avoid overbandaging) and ordered to give it again, but I do it quite often with no such problems.

Sadly i cannot reproduce it. I see that Hurl is having a wrong FirstAid animation, but do not actually perform it, but i cannot reproduce it from scratch, and thus have no idea whats wrong there.
I did found 2 minor problem with First Aid while trying to reproduce it, tho, and fixed them, so its very helpful as usual, man. One is about almighty buggy swap-by-X, that didnt updated FirstAid on a move; and other is about possible fail to update it for mercs affected by explosion. But those 2 is about wrong state of being affected (red crosses displayed on a portraits) by FirstAid (for example preventing bleeding or penalizing accuracy, as if being bandaged), not about wrong animation of it.

Ok, I think I know what happened and how to reproduce it. This is what happens if you press ESC shortly after giving an order to bandage. I must have done it thinking it may be too much and i would overbandage so let's maybe waste some APs first. So the problem is: in case of first aid (and maybe it also concerns some other actions?) pressing ESC in a "wrong" moment (immediately) does not fully abandon the order as it should. Most probably the animation is triggered first, seperately from and before actual action and so this state of semi-abandon is created. By the way, in this state you can't go out of it by pressing ESC again, but you can by moving a kit out of medic's active hand (for some reason it resumes to walking sprite, not standing one) or just by moving the medic. Sorry for the incomplete initial description, but I have realised it now, at the time of play my mind concentrated just on the result and I simply forgot the sequence of my actions.

Yes, thats great, i just never tried to waste APs that way, i used turn, crouch, or move, so was unable to imagine trying it. If FirstAid cancelled the time initial animation of kneeling is still runs, it doesnt stopped, unlike the actual action. And as later animation is tied with action, it act slightly odd when action is actually already stopped, as in this case. The one i found is directly related to FirstAid tho, so if some other actions are also act weird their separate way, they will still continue to do it.

Thats because animaiton sequence is broken by that time, its merely an another consequence of stuff already going wrong. I hope you joke about "sorry" here, tho. I simply dont know how to express my gratitude for that great help provided by you all that time, man.

I didn't mean I was going to waste APs by ordering first aid and pressing ESC. I had just immediately changed my mind from giving first aid to wasting APs (usually I also do it by turning/crouching). But then I must have realised ESC did not work and I saved the game to report a bug. What I did not realise was that the whole thing was caused by the first ESC, pressed too quickly.

Hey man, thanks a lot for your work, you just gave me a great reason to revisit one of my favorite childhood games!
While I have a lot of fond memories with JA, I also remember all the jank that came with it, so it's great to see someone fixing a lot of them (because the game still has a lot of charm).
I don't remember which sector it was, but I remember that there was a bunch of chain-explosions that you had to trigger in order to bomb away a bunch of trees and/or bushes to be able to get to a bunch of crates and I had to reload my save often there because the explosions wouldn't trigger properly.

I do have a question though, I saw you added a bunch of command line parameters and at least as far as I can tell they're all opt-in (so not active by default). Which ones do you personally usually play with? All of them, or just a couple of them? From readon the notes, I was curious to give all of them a try, I'm just curious if you have some opinions from playing with them.

Kind regards and keep up the great work!

Hello to you too.
Have no knowledge bout they didnt. There was bug fix from game developers in one of official patches, bit it was for other sector, 24.
I use {AIM AIR IMPACT GEAR INV} for games with armor and {AIM AIR IMPACT} for more classic feeling with armor bug (on Hard level, not on Go Ahead). I dont use healthy, cos it make game strictly easier (that is racionale behind theme, some bugs, that could be undesired to be fixed).
Dont forget they are not save related (unlike difficulty level), and could be turned off (un)intentionally.