I know problems with auto-travel have been around for quite awhile, especially with it taking your ship in the wrong direction. My issue is that it randomly goes into a fatal counter-clockwise circle and ruins my Tour of Galaxy runs. I run one Fed and one KDF ship daily and the failure rate is closing in on 50%. ToG is/was a huge source of EC for me. I'm not rich enough to turn over keys for EC.
I'll keep better track of when this occurs if I can overcome my frustration during the runs. The most recent failure was after my ship left Arawath, slipsteamed to Algira, stopped slipstream then attempted to auto-travel to DS9. The fatal circle left then started; targeting new systems did not work and manual navigation would not work either = ToG timer runs out & full mission is not complete. I suspect slipstream causes a complication but I need to see a lot more data to know for sure.