47-group cross sections and then merging them into 2-group cross sections using the get_condensed_library function

Hello everyone, I have a question to ask.
I am currently using openmc to output 47-group cross sections and then merging them into 2-group cross sections using the get_condensed_library function. When outputting on a per-assmbly basis, the 2-group cross sections yield the same results as the continuous ones. However, when outputting on a per-material basis, there is a significant discrepancy between the 2-group results and the continuous ones. Can you please explain why this occurs?
This assmbly comprises fuel, cladding, water, and poison materials.