This annoying bug is part of the old G3000, and this behavior and other bugs are fixed in the AAU1 update. However, only the Longitude and the HJet (and maybe others?) have implemented the update. The FlightFX VisionJet developers are still diligently working on it. The new G3000/5000 is fantastic, and I’ll be excited to see it in the VisionJet.
In the meantime, assuming you’re doing IFR routes with SIDS and STARS, you can minimize the probability of getting this by entering your SID first, then your STAR, and then any mid-term waypoints, making sure you don’t duplicate the SID/STAR fixes. Don’t use the built in MSFS flight planner, but enter your plan manually. And don’t change anything in your flight plan mid-flight.