https://forum.paradoxplaza.com/forum/threads/imperator-to-ck3-development-thread.1415175/post-30175504
https://forum.paradoxplaza.com/forum/threads/imperator-to-ck3-development-thread.1415175/post-30190466
and for legions as special troops it was because of the forced start date being much later than the I:R save date and the armies stuck with the I:R leader which got changed during conversation.
If the I:R leader is no longer alive/ruling at the CK3 bookmark date, the converter should either assign a valid leader or skip assigning a leader at all.