Hi @Audi86 ，
1.If you checked that there is no retention policy set, could you see if these sites can be part of Office 365 groups with expiration policy enabled? You can check it out through the following picture.
Azure Active Directory admin center: Azure Active Directory->Groups->Expiration
2.If there is no problem with the expired retention policy, you could choose to create a new retention policy for the site to limit system deletion. You could go through the following steps to set.
Microsoft 365 compliance: Policies->Retention->New retention policy->Edit the site scope used by the policy at Locations
3.If you find it inconvenient to create a new policy to restrict system deletion of sites, you could create a support ticket from the admin center and wait for a reply from Microsoft to respond back. since, we don't control the logs it's hard for us to troubleshoot from here.
Microsoft 365 admin center: Support->New service request
Microsoft official documentation reference on expiration policy：
Microsoft 365 group expiration policy
Configure the expiration policy for Microsoft 365 groups
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