The only time I've run into the Orca of incomplete missions is when I'm looking for more than one assassination target in the same system and I kill the first one. For some reason it gets confused and thinks both targets have been killed, even though it only updates the mission I actually did complete. Because both missions don't complete though, I'm still going to get the mission USS for it while it's active. The next time I drop into a USS that would give me the second mission's Anaconda, I get a junk ship in the form of the Orca instead, and no amount of beating that piñata will make it spill treats.