I have really only noticed this rare bug with Piriapolis and Land Bridge, however i don't think it is limited to these maps. Firstly, I always play titans.
The bug has to due with a LOS problem. What happens is (and this is hard to explain because it happens rarely) i will have a ship in the water. Now near that i will have a base, and in order to see blocks ahead of me i will build a basic 100$ soldier, revealing the sight in front of me, and then i will undo it to get back the money. However when i undo it the sight in the water goes away, including my water unit and the area around it.
1. To recreate this bug, play Titans on Priapolis against something other then Titans
2. Use ur soldier unit to capture the base
3. Wait enough turns (without doing anything) until you can build a ship. then end the turn again.
4. now send the ship out away from the base. Their should be 3 blocks inbetween the ship and the water baser, and it should be on the same level as the water base. Order it to attack whatever unit is nearby.
5. Now from your bottom land base build a mecha, and then undo it. You should no longer be able to see the unit untill the next turn.
edit: if you dont get what im talking about, i can take screen shots showing what happens.