This is also happening to me. Single player, Xbox. This is a save that reached perfection prior to 1.6. sometimes when I go to the walnut room it shows as yes, complete and I'm at 99%. Other times it shows no and 89%. I have not figured out a pattern to this.
Yeah same here as of today, last time I played 2 days ago on the update was fine, logged in again just (22:00 GMT) and had an update before playing (presumably the latest hotfix), now showing lower at 88%.
The upcoming Stardew Valley 1.6.16 rewrites the achievement/trophy code to work much more reliably (especially on PS/Xbox). In particular, the monster slayer goal tracking should now auto-fix itself when you load a save or connect in multiplayer.
Let me know if you still have any issues once you get that update.