Hi,
If there is some site unable to talk directly to each other if this case you should prevent the domain controller in those sites from registering its generic DNS record.
If you have a site able to talk with all sites ( hub site) , you should allow its domain controllers to register generic DNS record.
You can refer to the following link to get more details how you can prevent domain controller on branch site to register its generic DNS.
Don't forget to mark this reply as answer if it help you to fix your issue