There are some differences between the flight plan files (.pln) generated by Navigraph vs. the MSFS World Map flight planner. The MSFS generated flight plans contain waypoint altitude and speed restrictions. The Navigraph flight plans do not. The waypoint information is used by MSFS ATC to provide climb/descent instructions. If MSFS ATC is not used then this information is not needed.
SimBrief flight plans have the same issue. However, there is a workaround on the Download FMS page in the circled question mark (Instructions). “NOTE: After import you may need to reselect your SID, STAR, or approach using the provided dropdown menus.” Unfortunately most SimBrief users are not aware of these instructions.
Asobo/MSFS have been making changes to flight plan processing (fixes and enhancements) in recent updates. I don’t know if these changes are documented in the Release Notes. Apparently Navigraph is not updating their export processing to remain 100% compatible with MSFS. (Other 3rd party flight plan creators have the same compatibility issue.)
Using a Navigraph IFR flight plan without the necessary waypoint information for ATC often results in MSFS ATC issuing confusing and incorrect climb/descent instructions. Most users see this as a “broken ATC” that needs to be fixed. But MSFS ATC works correctly with World Map generated flight plans.
if requested I can provide flight plan files showing the differences between MSFS and Navigraph.