Hm, how do you mean "despawns"? W squads cannot spawn from anywhere except their entrance tunnels (not pictured), and W/GM can also eventually retreat there, but other bots will remain--there's no mechanism for them to leave or disappear. I notice over 20 turns pass between your screenshots there, so it seems kinda inconclusive at best. Can't really explain what would've happened without seeing it, but there shouldn't be any way to outright remove bots aside from them running off somewhere, and they will happily do that while you're busy doing/looking at something else.
Would need to see a video of some kind or more details to make head or tail of it, but based on experience so far I'm guessing there's probably nothing weird going on here...