One theory is that perhaps topic_users.bookmarked is getting out of sync somehow. If you have a problematic topic identifed, can you try to query the topic_users table for that user/topic combo you find, and see if bookmarked is true or false?
Also, I’m curious whether the new experimental /filter feature shows the “missing” topics with in:bookmarked, e.g. Discourse Meta. Can you try that too and let us know?