Ok. After investigation it seems like issues were fully on our side.
Site 2 and 3 had full autoupdate enabled. It was just it was first time we got email from them about update taking place.
Site 1 has security/minor updated enabled. And someone from other team did update it in June to version 6.0.0 as such all 3 updates were working as indented it seems.
Sorry for bothering you.
