For some reason, you have to have to hold shift in order to select multiple ships. This happens when you try to select multiple ships in a fleet in open space, orbiting a planet, or managing fleets. I'm not sure how many players will think of using shift to select multiple ships, but I think it would be better if you didn't have to. I don't think you should have to learn a trick to do something that basic.
The game should allow you select multiple ships by just clicking the ships. You click on a ship a second time if you want to deselect it.