I'm not hating on the game at all, actually I think it's decent.
But definitely some glitches.
Free flight mode seems to be ok with regards to this, but in career mode, if you change your flight plan the game gets the hump with you.
I'm trying to play them without using any of the super imposed guides, that I don't think.... You can turn off in career mode, so just using the aircrafts instruments as you would.
Several of the missions I've had recently are flying into Southampton. The ILS for that is pointed north/north east.
The flight plan in every mission it seems gives you awful pattern entry.
So if you amend your flight plan, it'll sort of let you do it. There is a nav point called PEPIS which lines up nicely.
So I add that waypoint, remove the ones it out, upload flight plan, file with ATC. On the map it looks all good.
But in flight weird stuff starts happening. Like it kinda thinks the old ones are still there, at the same time not. What the results is, is the stages sometimes get out of sync.
For example, I'm following the ILS, in approach mode, 2 miles from the runway, I've got ATC landing clearance, and it's telling me to land, at the same time the ATC is screaming at me to climb and maintain 11k ft......
I also had one occasion where I landed, I even followed the guided taxi way markers to the end point, and my mission requirement was still set a land.....that one also wouldn't let me complete the mission.