Okay now I'm not sure if this has been reported before or not, but sometimes when i tell fleets to jump to a planet one of the ships gets 'stuck' it keeps charging up and i get the 'going into phase space' type message but then something happens and it doesnt go anywhere.
i've very nearly lost a capital ship this way, when i brought up the actions the ship needed to perform (shift) i saw the waypoint was further right than the ship was but it didnt try to move to the point

Sory if this has already been reported but just a heads up