Today I came across a problem with accessing Owner custom fields (for the User object I had several of these fields).
I only could access few standard fields like Owner.Name, Owner.FirstName without problems.
SELECT Id, Name, Owner.Name, Owner.FirstName, Owner.Store_Name__c FROM CustomObject__c WHERE Id = :ourId
ERROR at Row:1:Column:74
No such column ‘Store_Name__c’ on entity ‘Name’.