Another lesser bug found: if a sleeper agent is a dog (might apply to all non-human characters) and gets ratted by another sleeper who got arrested, they will join the LCS but will keep their icon blacked out. This doesn't sound problematic but if you have a very large network it might be difficult to find out quickly who is in the shelter and has to be moved elsewhere.
Edit: this glitch gets cleaned up upon exiting and reloading the game.