By default Azure AD connect will synchronize disabled accounts from AD to AAD. It is normal and is it recommended due to Exchange hybrid and EXO requirements.

 

It is possible to create a custom rule on AD Sync rules editor to not synchronize disabled AD accounts:

https://spanougakis.wordpress.com/2016/02/28/how-to-stop-disabled-user-accounts-from-syncing-with-azure-ad-connect/

 

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