Some of these I've seen in other topics but drawing more attention to a problem has never been a bad thing.
1: Item comparison in some equip slots (the ships is what I noticed) just match the stats to whatever is in your inventory to what's equipped. I've noticed this on my shield slot and consoles mostly with a new item having the new name but listing it's stats as what was equipped.
2: Random chat pop ups mid-mission from NPCs. This has only happened to me in a group and I was wondering if it had to do with one member opening a box and everyone having to see it. It's happen a few times and it's never been anything I hadn't seen before. Really obstructing, whatever the cause may be.
3: Ship to ground transitions that place the wrong avatar on the wrong map. My captain in space, my ship on the ground. The game usually takes a bit and fixes it but on away missions it keeps the rest of the team from beaming down and forces you to abort and retry in the hopes the right guy gets beamed down, which may take a few tries.
4: Renaming a bridge officer doesn't stick. Next time you log on it's back to what it was originally.
That's all I can think of right now other than a few awkward things I'd like to think will be fixed up by retail like a lot of the item description being code along the lines of AIchance_whatever Other wise this seems to be on it's way to being a real enjoyable experience.