Hello, @nevercora
Qualifying places are determined by nation club coefficient, not league reputation.
Looking at your save we can see there is a lot of editor files in use on the save, one of which is affecting Asian nation rules, which disables the coefficient system for the continent (see how Europe's qualification places can still be seen under Nations > Qualification places as these rules haven't been edited).
When running a new save in Asia, we can see that the reputations are changing, so this seems to also be editor file related. If you send a new save from the start of the game we can take a close look, but this does seem to be due to edits, not a bug, thank you.