I’m a bit unclear on what you are asking: what if the transaction broker is the seller’s agent while the buyer has his own transaction broker or single agent or what if the transaction broker for both is actually looking to the interests of the seller instead of the transaction?
The first scenario is perfectly acceptable. The second is not. A transaction broker should treat both parties equally. He or she owes the same level of service and diligence to both parties without preference. If they are giving representation to one party over the other, that is certainly something to discuss with that agent and his broker. That’s what I would do.