I have experienced the exact same problem.
I’m using the Development version… updating it before every test flight (rebooting MSFS too).
(1) Create a flight plan in Little Nav Map
(2) Export the plan to MSFS
(3) Load the plan in MSFS – Check it: looks perfect before hitting ‘Fly’
(4) Check the plan in the MCDU – it is mangled; new waypoints inserted (where did they come from?)
(5) The ILS plan is not followed – strays from last non-approach waypoint to going directly to destination airport – must manually fly the approach.
(6) TRY FIXING THE PLAN IN THE MCDU: Erase waypoint function does not work!