Last version of bukkit "PermissionsEx v1.23.4" causes problems with other plugins and does not let users enter, expelling them after the attempt to enter and the latest version https://ci.yawk.at/view/PermissionsEx/job/PermissionsEx gives this error in console.
https://hastebin.com/pokudimano.vbs

Server version 1.12.2

All the best.

I have been running PermissionsEx v1.23.4 for a few years and I upgraded to the latest bukkit version as they were released, I'm currently running 1.12.2 and don't have any issues with PEX. Maybe its the other plugin or PEX not being setup right.