Patient: "Doc, it hurts when I move my arm like this"
Doctor : "Don't move your arm like that!"

In other words, don' go to flank for the rest of the patrol.
Seriously:
Do you have SH3Commander?
If so, are malfunctions enabled? If so, it may be a malfunction of some kind. That is the only thing that I can think of.
I've had the same problem a number of times before.
IIRC the problem went away next patrol. I just had to keep in mind not to go to flank or crash dive(the engines go to flank when you hit the C key). Not a bad enough malfunction to abort a patrol and return to port with.