This major bug that exists since the start of the sim.
I report it here and hope we'll get some feedback and a fix soon.
The issue is that the sim chooses by itself to remove some waypoints when loading an approach or when an approach is already loaded.
This SHOULD NOT OCCUR in the real world. This is the pilot's decision to remove a waypoint or not or to bypass it by direct to or activate a leg.
Here are 2 examples to reproduce that issue, both tested with no mod and with the TBM900.
Example 1 (approach loading):
From the world map, choose LIMF to LFMN.
When in the cockpit, adds the SID TOP6B transition ASTIG.
Then add the approach ILS4L transition AMGEL.
At this time the sim removes some waypoints of the SID.
Example 2 (approach loaded):
From the world map, choose LFRK to LFRN.
When in the cockpit, Add the waypoint GILRA after LFRK.
Then load ILS28 transition SAMPO.
Then Add the waypoint LEMAR before the waypoint GILRA.
At this time the sim removes the waypoint GILRA.