This may appear to be a bug, but it's a consequence of the game's reinforcement feature. If a vacant Deposit is reinforced by Defensive units rather than captured with Offensive, it's not considered to be "taken", and will show up as a vacant one on the Radar. This "Deposit Trap" strategy is commonly used by Clans to gain XP. Be sure to send recon drones to a Deposit before deploying your main forces – if it looks too good to be true, it probably is.
Another possible scenario is someone else sent an attack to capture a Deposit and their units arrived minutes before your forces.
Another possible scenario is someone else sent an attack to capture a Deposit and their units arrived minutes before your forces.