פירוש על ברכות 44:18

[HE] WAITS UNTIL THE URINE CEASES. We will learn later that when one prays in the presence of urine his prayer is invalid. If so, how can the Braiso say that after he finishes urinating he may continue his prayers? The Braiso is speaking of when one is urinating on the earth or on clothing, and the area where the urine is falling is not damp enough to moisten something that comes in touches that area as can be understood from the Gemara later on 25a. For example the flow of the urine was drop by drop so that they are immediately absorbed in the ground or clothing. So did Horav R’ Yosaif explain our Gemara so that it should not contradict the later Gemara that says that one may not pray in the presence of urine. That Gemara is speaking where the urine is moist enough to moisten something else and our Gemara is speaking where there is not enough to moisten something else.
However, it makes more sense to say, that even if there is sufficient urine to make the area moist enough to moisten something else, it is permitted to continue praying. Since by Torah law it is only prohibited to pray opposite the flow of urine, as one is urinating, and it is the Rabanan who decreed the prohibition to recite Torah in the presence of urine even when one is not urinating. And since in this Braiso, he is already standing in middle of his prayer, the Rabanan did not trouble him to repeat his prayer.