Transports: I've noticed that when a unit gets off a transport, it still looks like it's on the transport and cannot fire any weaponry if it couldn't on the transport.
Nuke launchers: I'm not sure if this is purposeful, but a nuke launcher (structure, submarine or battleship) can only fire once. The launcher never closes and it never registers that it fired. SMD can also only fire once.
If these are bugs, I just want to bring them to light.