Some secrets simply aren't registered by the counter, even though I'm 100% sure I got them all, even the last two in the expansion pack. I'm even doing a new complete playthrough with multiple saves to make doubly sure, but they still won't register. Does anyone else have this problem?

EDIT: two more registered, but still nothing on the last two.

I had the same problem, I had two that didn't count. I went down the list of secrets and visited every secret again, bumping into every corner just in case it was only triggered by entering a certain 'sector', and eventually they all registered. For me, the missing secrets were both in episode 4. Probably the only way for new players to avoid this is to immediately check if the secrets counter goes up or not when going to a secret area.

The secret counter is for sure bugged. Mine was stuck at 18/20 all the time. You can still get all the achievements though.

Missing two as well and when I re-entered one of the secrets, the counter went up to 19, only to go back to 18 after loading a save.