I am occasionally losing my troops during an invasion. The AI launches a troop ship from the planet I am invading, the invasion never continues and I can't get my troops back. I have seen this happen at the start of an invasion, as well as part way thru.
Also, when I make some of the new ship models, namely the Aegis cruiser, the fleet model becomes a collection of fragmented parts. It's also very large and makes planet selection difficult.