I've had that happen on several occasions too. I've been sailing straight towards a waypoint but instead of moving onto the next once we reach it the u-boat just starts going in circles.
If I move the waypoint further away from the sub the same thing happens, we sail straight towards it and back in a circle again once we reach it.
If I delete the waypoint using the rubber tool we just end up going in circles at the next waypoint.
I have to delete all waypoint in the course and plot them all again.