I had the same problem as the OP, but only when playing TEC -- my group (chock full of flak, light, scout, and siege frigates plus a few light carriers, marza and kol battleship) was set to group move, and I told it to attack a neighboring planet.

Note that the "group" in this context was actually comprised of 2-3 "fleets" in the game sense

When I went back to look at how things were going, only the marza had jumped... the others were still lingering in the original planet deep in the gravwell.  I can only guess the tardy fleets were getting into formation before proceeding, but still -- no ship  should have jumped until all the ships in the group were ready.

I have not run into this playing vasari or advent.

I should add that I have only recently (last game or two) started actually using game "fleets", so perhaps that's why I haven't hit this behavior as advent or vasari.