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If there are multiple entity types that are group, views relationship to the og group will join on incorrect data.
node are groups.
customeentity are groups.
The views relationship with gets the og_membership generates the following SQL:
LEFT JOIN og_membership ON (customeentity_og_membership.id = og_membership.gid)
Which returns both the og membership for the desired customentity, and the og membership for a node that has the same id as the custom entity.
The SQL generated should be:
LEFT JOIN og_membership ON (customeentity_og_membership.id = og_membership.gid AND og_membership.group_type = 'customeentity')