Today, my players found a problem. There is pvp restriction on every spell. Almost all of them are unusable. I don't know how this happened, but they are all this way. How do I fix this?

Seems odd, did you enable a WorldGuard pvp flag for the whole work or something? If you need to turn it off completely you can add this to your plugins/Magic/spells.yml

override:
  parameters:
     bypass_pvp: true

That will allow pvp with spells even in areas that disallow pvp.

I'd be curious to know what exactly happened, though.

Did you figure out what was going on here? Did the pvp bypass fix it?