yiit they began logging the IP of a user. Meaning they actively were monitoring them.
Proton actually has a feature to do this, so you can see if anyone else has been logging in to your account, but presumably in the case of a request from LE they would do it secretly and without user consent.
The thing is, anyone with a serious threat model should understand that a website you visit will be able to see your IP address if you don't use a VPN or Tor.
LE knows this, and so they ask Proton to provide it. Proton can't just refuse a legally valid request when they obviously have access to the data requested.