I've encountered their containment chamber in the beggining of the game, do you have it too, or it just a bug I only have ?

I've found 079 in the LCZ, but I've seen him there in earlier versions.

I found the 106 containment chamber in the light containment zone the first time I tried 1.0.
Memory is a bit hazy, but I believe I also found the elevator leading to the Plague Doctor in LCZ, but that I can't be sure of.

I've had missing checkpoint zones. I'm sure they'll fix it soon. Minor bugs in the map spawning code I guess.

Two Heavy Containment Zone checkpoints spawned, and both lead to the Office Zone checkpoint. This seems to happen 1 in every 4 map seeds for me.

Yes, 079, 106, and 895 appeared in the LCZ for me as well. I've tested this on a Windows 7 OS Acer Laptop (1.8 GHZ processor and basic Intel graphics). What's more annoying though is that (not a bug though I guess) 970 is making me dizzy. I used a random seed for this (didn't know what).

I found the cause of this bug: This is what the game uses to know if it should place a checkpoint room. This doesn't work very well, and makes some rooms appear in the wrong zones. It can also cause bugs like this: A better way to do this is use the GetZone function: