First off, love Rebellion. I simply cannot wait to see how the other races get updated.
This is mostly about minor issues that occur that do not directly affect the gameplay, but occur often enough to become a pest.
1. Jump Canceling. - There are several times, it has happened with the Titan as well as the various other ships, I set them to jump to the next planet, they head towards the edge of the gravity well and then sit there. When you click on them the order you gave to jump is gone and you have to tell them to do it again. It doesn't happen 100% of the time, but well enough to become noticable, especially when you are attempting as to leave a planet.
2. Novalith Cannon Autofiring - I noticed this in the past with the old Sins, still kinda seeing it now. If i don't turn off autofiring on the Novalith, it will shoot until I scuttle it even if I take it off auto-fire. I am not sure if anyone else has had this issue, but I can be annoying since at that point I can't even change its target. I was playing with a roomate and when he finally cleared a planet and colonized it just seconds before my Novalith hit it. I was his teammate.
3. Alerts and Warnings - Is there a way that the alert can be set to what constitutes a threat? Many times I get the warning of an attack to find a single Cobalt frigate ( With no fleet behind him in support ) chilling in the same gravity well as 3 hangers, 3 repair platforms, a multitude of gauss turrets and two fully upgrade Starbases (As loyalist). Not necessarily a gameplay issue, but it could fall under annoying. Either the little frigate is packing some heat I should probably know about, or he is technically not a threat, and he would be euthanized shortly. This simply is annoying.
4. The AI. - A pain. I know you have heard this before in other posts, just wanted to put it out there. Four perchons, 3 cobalts and a LRM isn't going to cut in mid-late game for an actual attack. I get probed dozens of times in a 3 minute span and thats what they send me. I play with the AI set to hard BTW. I will note though that more than once people have quoted that they sit and build up planets, and just sit there, I have noticed this too. Like one AI had 5 Novaliths going at my planets at once. From the back end of there area. Smart and efficient on their part, kudos for effort, but fun-killing especially as fast as they get them built and firing. Also, every ship runs from a Titan except Capitol ship. I have attacked a planet in what all the defenders except an Akkian had started booking it for the other end of the gravity well as soon as my Titan jumped in. Not very sporting.
5. Scouts. - Most often with these guys I have noticed the failure to follow a jump command and sit on the edge of the gravity well (Unless they are on auto-explore.) Also, when sent via wormhole to a new galaxy and asked to auto explore, without fail they immediately set course back through to wormhole to the parent galaxy to explore, even though I may own the entire thing anyway. A huge pain especially when I know there is a Novalith somewhere in that star system, and I would like him to scout it out before it starts firing at me.
6. Artifacts - It could just be random chance, and mostly likely due to misfortune rather than actual game issues, but these tend to cluster heavily. For example an enemy AI found 6 around his home planet. Then he Nova-bombed me to death shortly after. I know you shouldn't rely on Artifacts too much, but as a fun item that can give an edge to someone, thats just bad. I have had this happen twice now.
Note I make this thread of minor items that are currently occurring. It is my intent to convey possible problems, not speculate on solutions. These may not be problems at all, but all user error, or possibly as intended. I do not desire to make this a *This is what would be cool to have instead of That*There are plenty other posts doing that 
Simple little twitches here and there. Plain and simple.