this has happened a few times to me with a letting agent paying me and then the landlord sending a cheque for the same invoice.
i always return it as honesty usually is the best policy in this scenario
a few years back i had this landlord going totally mental at me down the phone cos the letting agent had payed me and he had sent me a cheque , his error tho.accused me of all sorts and was really aggressive. i played it nice and calm and could not have been more pleasant to him, went through to my office found his cheque in the in tray, checked the invoice was payed etc etc. told him i would return his cheque as a matter of urgency and if i ever crossed paths with him again iwas gonna go to his office and nail his f***** ear to his f***** desk.kinda stopped him in his tracks. ha ha....i usually get on well with my customers tho