I just noticed that when I am watching a episode and the next item is a special episode it does get skipped and plays the next "normal" episode instead.
Example: I was watching S03E11 -> Special -> S03E12
At the end of E11 the ATV app skips the special and goes straight to E12.
On the WebApp, iOS and Emby for Android it gets played properly E11 to Special.
Ebr, if you need a log (server/atv) just let me know.