If the Anime has both "regular" and special episodes, they should be IMO counted separately. For example, I have 12 of of planned 26 GITS:SAC episodes, plus 3 short specials. Mylist main view have GITS:SAC listed as 15/26 episodes, which is wrong (or should I expect 29/26 when I get all the episodes ?).
My prefered solution would be just not to count specials as episodes at all.
this is a general problem.
and there is no easy solution, bc i.e. specials might also be the same eps but in a different package (i.e. S1 being a vcd with the first 4 eps).
/me still hasn't found a perfect solution for those problems.