When a Rapture uses its dominate skill on an enemy frigate (causing a permanent conversion to the Advent), the frigate's original orders go unchanged until you provide new orders.  While this may seem like a very minor issue, it provides an unusual problem for the player: if the ship was ordered to jump away, it will continue on its course to the edge of the gravity well, jump, and usually get obliterated by its former compatriots.  This is especially problematic in very large battles with domination set to autocast, as it's often quite difficult to pick out which vessel has been dominated.  Otherwise, you could simply click on it and hit <stop>.

I thought it was somehow fixed in a prior version, but I can't figure out where it was that I saw it (maybe just in my imagination).