it seems like a recent change in either Emby or the Trakt plugin have caused some issues with syncing of files containing two or more episodes. Emby is still correctly identifying such episodes, but the Trakt plugin no longer marks the episodes as collected when synced to Trakt. In the scenario where you have a file called "One.Episode.S01E01E02", the Trakt plugin will mark "One Episode S01E01" as collected and skip "One Episode S01E02".
Emby version: 126.96.36.199 (note: beta)
Trakt plugin: 188.8.131.52