oData query raises an error when you use a complex type field as a condition.
The following query will raise an error:
XRMServices/2011/OrganizationData.svc/AccountSet?$select=Name&$filter=PrimaryContactId/LogicalName%20ne%20null
The following query will raise an error:
XRMServices/2011/OrganizationData.svc/AccountSet?$select=Name&$filter=PrimaryContactId/LogicalName%20ne%20null