I have a few games with similar situations, but it's usually someone at war with me moving ships into the same location I already have others at. (In one case, the Drengin were attacking a stack of six transports, one was destroied, then the Drengin battleship moved under the other five and was unattackable until I move my ships out.) In that particular situation, the solution is simply to move all of the ships one space then attack.
A stopgap solution to the problem while waiting for it would seem to be to aquire the ships of one race and move them out yourself. If it happens often enough, you might even be able to assemble a significant sized fleet without maintinence. (Which reminds me, are the battleships from anomolies, and combat ships aquired from other races, supposed to be maintinence free?)