We are experiencing the same issue in Moodle 3.0.8, I left a comment in the Tracker, but it looks like someone will need to create a new one as I'm unsure if devs can reopen it.
We have a similar error in 3.1.6, limits are set but exceeded, i.e. set for 4 but 7 students allowed in.
Have I missed something?
Thx