Looks like the users previously were being  added as 
u...@domain.com@localhost.com.  I deleted those accounts manually in the 
mongodb and updated the Search base to 
(&(objectClass=user)(sAMAccountName={0})) and it seems to be adding the 
users correctly however the ldap synced users cannot log in.

I updated the search base to (&(objectClass=user)(UserPrincipalName={0}))
Seems to be working fine now.

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