I hate when companies mislead, they claim email encryption. but the question is how they know the email is suspicious. it means they monitor emails and obviously, Proton Mail is (not) the trusted choice for secure and private communication.
What email was suspicious? From what I can read. Proton provided the Spanish authorities with a recovery email address, which the latter then used to find an associated Apple account. While I agree this makes Proton unreliable for many things, there's no indication they were reading any emails.
No service can read all emails of a platform, but spying is still not good anyway, if someone is misleading it's a government problem to find and punish them, communication should be safe anyway, old face-to-face communication is good then internet.