For our brain this arrangement of parts is especially tricky to process and we must take good care when learning such episodes in our organ pieces. The best advice would be to isolate the manual and pedal parts and practice repeatedly and separately.
Let's say that your difficult passage extends over 4 measures. So I would recommend you practise pedals alone 10 times in the tempo which is about 50 % slower than the concert speed.
You will notice that at the beginning repetitions are quite shaky but the 9th and 10th repetitions feel quite secure. Then practise manual part alone. If it is polyphonic, play the hands separately first, repeating 10 times the left hand part and 10 times the right hand part.
Once you do that, you will be ready to combine the right hand and pedals, and left hand and pedals. It is important to go on to the next step only when you feel like you are ready and feeling very secure and your playing seems quite fluent.
Otherwise frustration soon kicks in and real progress would be very difficult to achieve. But if you patiently wait when this combination becomes so easy, that you can play it very slowly without thinking, automatically, then you are ready to go on to the next step.
This way you can master even the most dreadful looking pedal parts going in contrary motion with the hands. Remember that for many right-handed people left hand and pedal combination takes longer to master. Nevertheless, the process is the same - isolate the problematic episode and practise solo lines and each of the available combinations before putting everything together.
All of the preceding advice won't work unless you figure out the fingering and pedaling in this episode so make sure you do this first.
By the way, do you want to learn my special powerful techniques which help me to master any piece of organ music up to 10 times faster? If so, download my video Organ Practice Guide.