I have not seen any posts on this subject after a quick scan, so here is my experience. My capital ships, I mainly play vasari but pretty sure it applies to all races, have some pathing issues while in fleets.

The first one is when trying to navigate across a sun's well. The leading capital ships goes around the sun fine and jumps away. The other capital ships usualy fall behind a little then try to go through the sun and get kinda stuck, moving very slow as they keep bumping on the inner edge of the gravity well. If the move destination is prety far away they are pretty much lost for a long time, unless I give them a sequential move order around the star.

The second issue is with wormholes. Sometimes my ships get stuck in the space between the entry and the exit and just sit there. I can try to stop their order and give them new one, move the rest of the fleet back, and other things but they just sit there. Sometimes I can get them to move back after repeatedly giving them move order, but they move very slowly and can take forever to get back to "normal" space, So issuing move orders across a wormhole is very risky, and kinda defeats the purpose of using it.

This pathing problems usualy occur later in the game when I have 4-8 capital ships in my fleet. The funny part is the fleets leading capital ship always moves fine and gets to the destination ok. Also all the cruisers and other smaller ships in the fleet are ok, but the rest of my capital ships just get lost. It is a pain when you try to defend or attack and when your fleet gets to the destination there is only 1 capital ship there.