Its on your customers not giving enough information in their wire transfers. That's something thats chosen when you initiate the wire, there is plenty of space for the information you request.
There are several ways to reduce the problem at least, all by accounting and billing methods. On accounting, there should be amounts sitting out there in an account waiting to clear for the incoming payments. The ambiguous payments are a small subset of the total and will likely be identifiable simply by amounts outstanding for smaller quantities. If you have too many duplicate amounts with ambiguous payments, and you have less than 100 frequent wire clients with this issue, you could implement collective invoicing on a monthly basis for those clients, something commonly managed by the collections dept and part of key client management anyway. That would significantly reduce the quantity of incoming payments and also make them more unique values. You'd still have to call to verify payment, but this way you could call the client directly instead.