Hi @DSmetko,
How are you verifying that these contacts have been deleted? HubSpot search can be moody sometimes. If you searched for email addresses via the search bar, I’d recommend double checking again on the contact index page (Menu > Contacts > Contacts).
Next, I’d recommend checking whether these contacts are still in the bin. Could you check whether they can be restored?
If they are in the bin, it’s a matter of figuring out who brought them there. If it was not a user, it might have been an integration. Under Settings > Integrations > Connected apps, is there any app which might be updating (and deleting) contacts?
Best regards!