2) Statement made by agency
Although it does not happen very often, agencies or representatives of those agencies may (by accident) have stated to you they represent the landlord (as well). This statement can also be made implicitly. An example of this is when in the tenancy agreement, or letter of intent, the same agency (or affiliate) will act as the administrator of the contract (and thus acting on behalf of the landlord and representing him). The possibilities are endless
The statement does not have to be in writing, but evidence wise it would definitely be better to either have it on paper (including e-mail) or a voice record, or else you as a tenant will solemnly trust that the agency will confirm to the court they made this statement to you before, and in doing so confirming your claim. Indeed, this is very unlikely and will not happen. But hey, in theory, everything is possible.
3) Statement made by landlord
If the landlord himself states that the agency in question is representing him, the statement itself may be enough to be admissible as evidence. It is not necessary that the landlord paid anything to the agency.
Frequently heard excuses made by agencies
These following excuses are often made by agencies not having them to pay the agency fees back. Any one of them is not a legitimate reason why the tenant should have paid the agency fees.