I'm trying to add timed permissions to a player with:

/pex user (user) timed add essentials.fly 100

But it's not working, when i put in console, it says:

23.08 20:13:09 [Server] INFO Timed permission "essentials.fly" added! 23.08 20:13:09 [Server] INFO User "559b824e-edc3-3c29-a21f-257e11905dfa" get timed permission "essentials.fly" for 100 seconds from CONSOLE

But the player still can't using /fly, what i'm doing wrong?

Unfortunately PermissionsEx is currently unmaintained and no further updates are planned. Because of this, all pull requests are being closed. If you are looking for an actively maintained permissions plugin, take a look at LuckPerms. It is compatible with major server platforms and can import data from PEX.