The more serious of the two bugs I've encountered it what I'm calling ghost ships. The ships show up when you are zoomed out to the system view:

But when you zoom in to the planet view they are not there:

When scuttled the ships are destroyed and supply is freed up. This has only happened with Kodiak Heavy Cruisers. I have a saved game where this bug is present for me and an AI opponent if there is a need for that. I have been getting some odd behavior with the move as a group command so it could be related to that.
The other bug seems to be related to the faction specific achievements I was unable to get the Ensign and TEC Fleet Diversification I assume this is related to the TEC faction being split in two. I was also unable to get Squadron Leader.