I first noticed an issue with specials while trying to watch the show Gravity Falls. In season 1, I have several of the specials, all of which are supposed to be included at the end of the season according the TVDB. However, when watching an episode, for example s1e5, the 'Next Episodes' section displays specials starting from s0e6 until s0e17 (all of the specials I have), then continues to s1e1 and so on in numerical order. If I open s1e17, the next episode list starts at s1e1 and continues in numerical order.
Looking at the season list, I am seeing all of the specials listed first, instead of last.
I then wanted to check a show that does have specials after certain episodes, so I opened up Doctor Who. When I look at the season 8 listing, I again see all of the specials listed first. Clicking through to s8e3, the Next Episodes section is showing s0e131, s0e132...s0e143, s8e1...In the same fashion as Gravity Falls was showing.
I've double checked the meta data, and the specials do match the appropriate before/after markers; and they do list correctly when viewed through the webapp.