This is happen to me a few times now. When I get halfway thru the level, I'll make new towers and they just disappear. They're invisible and don't fire, but I can still click the area and access the upgrade menu. If I build a new one over them or finish the level, the game freezes or crashes. Here's a recording of it:
+1. I've never made it through a "night" mission without this happening. You can get through the level, but EVERY time you place a tower, you have to place it, click the invisible tower, sell it, then place (and pay for it) again.
The only work-around I've found is to close the browser tab and reopen it after every night mission.