This happened multiple times when I was testing my map.
In said map, I have certain enemies with a mobility factor of -1 to render them immobile so that they can take on a defensive role instead of abandoning their post and rushing you like they normally do.
This glitch seems to occur when a mobile enemy runs into the immobilized enemy. What happens is that both entities and their weapons disappear into thin air. I have checked the triggers and everything and there do not seem to be any trigger actions or errors that can cause this to occur. So I have concluded (for now) that this is a glitch in the Matrix.
But what happens next is even more problematic than the disappearances. For some reason, after this glitch occurs, all enemies on the map will become pacifists. They will still notice you and jump around, but they will not attempt to shoot you. I don't see the weapons they are holding go through their firing animations, so I can only assume it is the characters themselves who are bugged. Since I have PSI blades disabled on my level, I currently don't know if the enemies will or will not slash at you instead. You can still shoot them and basically slaughter everyone if you want to. This does not seem to have an effect on your allies, at least when strict casual mode is enabled. They will still act normally and engage the enemies.
So you can see the problem behind this glitch. The most obvious solution would be to get rid of mobility -1 enemies. If you know of another way to fix this problem, then leave a reply. Thanks for noticing.
TLDR;
Enemies disappear when they collide with another enemy with -1 mobility factor. All other enemies in the map refuse to attack you with guns afterwards. AI controlled allies still try shooting everyone.
EDIT!: I deliberately body slammed one of the enemies, and it seems what happens is that you get transported out of the map, fall to the bottom, and die. Huh.