The one starbase cap is to prevent one player from being able to build said four starbases at a single planet. It works much the same as the mine slots. There's a limit, but it applies seperately to each player. It's perfectly reasonable, in my opinion, to have allied reinforcement, via starbase. If you had a teammate, or multiple teammates, well, you all go. Late game fleet beats late game starbase, ne? Multiple late game fleets beat multiple starbases. The point of locked team games.
And if they've got their fleets in support, those fleets are not elsewhere. Attack elsewhere.
Basically echoing most of the other posts in this thread. This is not a bug. Building starbases in wells you do not control is a valid part of game strategy.
And besides, think of the cost of deploying and upgrading a starbase. If an ally does this in their allies' well... Their not doing it in their own.