[2.2.10 and next] Special stage tokens are "eaten" by alternate exits
This was discovered in SRB2 the Past via the level Emerald Coast of the SRB2 Christmas Campaign.
In this level there are 7 tokens, a normal exit, and an alternate exit earlier in the level that takes you to Sonic's Nightmare. The detail that matters here are the tokens and the alternate exit as collecting a token and then going to Sonic's Nightmare causes the game to change the next level to be the alternate exit's target instead of a special stage. However, this can happen on other levels with alternate exits too.
I have prepared an example map to better show case this bug.
If you're wondering, completing the replacement stage while still carrying the remaining tokens will allow you to go to the special stages as normal.
UPDATE: This issue is confirmed to still be present in the next branch via the srb2win-udmf-triggerer.exe