"Spy bots aren't allowed to spawn in respawn room areas. The space behind the gates of Mannhattan is considered the blu respawn room. So why do spy bots sometimes end up spawning behind Gate A?

The nav mesh marks areas as "RED_SPAWN_ROOM" or "BLUE_SPAWN_ROOM" based on whether the area intersects with a func_respawnroom brush entity.

The author of mvm_mannhattan apparently decided to add a hallway to the left side of the back of the Gate A area for bots to spawn in, and they must have made the decision to add that area relatively late in the process, because they didn't actually bother to extend the func_respawnroom to cover it.

The blue outline in the Hammer top-down view shows the outline of the room. The red outline shows the func_respawnroom brush."