Yes, when a partial payment is applied to an invoice, this resets the maximum payment for the particular invoice to zero. This was intentially designed in the program, because if an invoice is not fully paid that typically means that there is something about the invoice that requires attention and that you don't accidentally pay the remainder until you are ready to.

So whenever the message 'Applied amount cannot be greater than the maximum payment' appears for payments, it means that the maximum payment on the invoice requires adjustment - usually increased to the desired amount to pay.