I've had a problem with adding ships to a fleet that's already formed. Here's what normally happens. I have two mediums already in a fleet and I'm trying to add another, so i select both and click the create fleet button and nothing happens. I end up having to disband the first fleet, move all 3 to another square and create a new fleet. I'm sure other people have reported this problem.
I also don't know if the second is really a bug, but when ships are in a stack I can't access the detailed commands for them, like with Constructors, I have to move them out of the stack to build a starbase. I don't know if this is a bug or design, so please tell me.
Third, sometimes when I'm upgrading a class in Ship Design I'll rmove a part, only to have it reappear the next time I put something on. This has only happened once, but I had to go in and design it all over again. The Clear button didn't work either.
Anyway, great game, these are actually my only real problems with it.