Good to hear you are finding worthwhile pursuits during the lockdown. Those are interesting results.
If I am reading those plots correctly, you are seeing a 10%-15% difference at the red end of your instrument response when using either Castor or Regulus. That is quite a substantial difference. Assuming the instrument response from the 2 stars were calculated on the same night and under similar observing conditions, were the altitude of the stars similar? If not then the differing effect of atmospheric extinction with altitude might be the cause, though even then I am surprised by the size.
Another possibility is somehow the slit isn’t being uniformly illuminated by blue to red light. This might happen due to atmospheric dispersion. The atmosphere can start to split the light of a star just like a very weak spectrograph, so you capture more blue or red light depending on where the slit is placed on the stellar source. You could get a similar result with telescopes that contain lenses if they don’t bring red and blue to the same focus.
A way to test for this would be to compare results between a wide and a narrow slit. A very wide slit should capture all of the starlight even if it has been chromatically dispersed by the atmosphere or lenses. While a narrow slit might record more blue or red light as you move from target to target, or across a single target.
Just thoughts, and I’ll be interested to hear what others think.
Assuming there is no reliable way to correct for this, then I agree cropping the spectrum is a good approach.
Keep safe and well,