I've been having this problem since v1.0, but haven't seen it reported at all. There are two seperate bugs that I've noticed and have continually been dealing with.

1) Rogue ships - If I have a Frigate Factory building ships that auto-join a fleet in the same system, the last ship build almost always ends up having a mind of its own. I can select the fleet icon and tell the fleet to move to any system on the map, and that last ship will ALWAYS go back to the system with the frigate factory. I can jump in the middle of a huge battle and that ship will still turn around, plot a course for home and run. The only way to avoid it is to manually remove that ship from the fleet and join it up again. I'm not sure why this happens, and I'm 95% sure it's been reported without me seeing it, but it's pretty annoying.

2) Rogue fleets - This problem I've encountered with much less frequency, but when it does happen it almost always seems to do so at the absolute wrong time. Sometimes when I select 2 or 3 fleets of ships and tell them to jump into another system, one of those fleets will issue itself some random order to march off to another neighboring system after completing the first jump order. The other fleets will continue doing what I told them to do, but that rogue fleet will just plot phase jumps and shoot off into another random system unless I stop them (and I usually can't in time before most of them leave). I've had this happen when attacking enemy systems, when retreating (the rogue fleet will fly directly back to the system I'm running from), or when moving fleets into position to defend a system. It can be ridiculously irritating and inconvenient. I don't have a video, but it just happened to me again and I lost a leveled up Kol as a result.