iraf.net

I am trying to reduce some spectra data and the process seems to be going fine until I run the apall task. When I run apall I find that some of the orders have this issue: https://imgur.com/a/xY9c08c
As you can see the order falls off half way through the order. This only happens for some of the the order. It happens on the 21st order then doesn't happen for a few then happens to a bunch of orders around 30 then stops happening again.
My reduction process is roughly as follows: I subtract the bias, then find the apertures in apflatten, divide the flatten flat from the science data, then appscatter, the apall. Any help would be appreciated because I can't seem to figure out how to fix this or even why it is happening.