Update
It was informally confirmed to me that the reason for rejection is affiliation with a sanctioned institution. The publisher complies with international sanctions, and the journal follows the publisher's rules. Working with editors and reviewers from sanctioned entities does not interfere with the publisher's policies.
The restrictions are not mentioned on the journal's website, nor were the reason for rejection explicitly stated in email. This was my source of confusion.
My paper was 'found not suitable' by a journal director. I suspect this decision might be based on one of my affiliations, which is currently sanctioned by the US (not sure about EU), although the journal itself is EU/CERN-based. There is no mention of any submission restrictions on the journal’s website, and they even have a non-discrimination statement. Here are some reasons for my suspicions:
Fast Rejection: The rejection letter was on the same day, which didn't allow enough time to process it.
Source of Rejection: The rejection was issued by a director, not a topical editor.
Relevant Publications: The journal has previously published papers on related topics.
Previous Rejection History: My paper was previously rejected by another (more reputable) journal after the third round of review.
Undisclosed Source Information: I have information from a source I can't disclose that the rejection is based on my affiliation.
It also seems that the journal has no issue with editors and reviewers from my organization.
My question is: should I reply to the journal expressing my concerns?