I am glad you are finding the tutorial useful. While ISIS is great for bulk reliable processing, BASS is very flexible and relatively easy to use.
Robin gives good advice on the hot pixels. Similarly I would suggest trying to locate the position(s) in one of the raw spectrum images, then compare that to your master dark frame. When creating a hot pixel map in BASS, you should use your master dark frame, that way you do not need to worry about clipping out any of the spectrum. Then you simply apply the same hot pixel map to all images.
If it turns out to be a frame specific problem, probably a cosmic ray hit, then the BASS “Cosmic, Hot & Cold Pixel Removal” tool allows you to select any size of sub-region to work on and set the threshold. If it is on a single image you could zoom in on the problem region, setting a very small rectangle around the hot pixel, and set the threshold to just pick out that pixel. How well this works will depend on whether the pixel(s) stand out above the spectrum intensity. There is also a tool for editing 1D profiles, but this really should be used as a last resort, and I would be tempted to ditch the sub-frame is there is a low intensity cosmic ray hit that is proving troublesome to remove.
That is a useful workflow you have shared. The one bit that jumps out to me is whether you are applying identical rotate, tilt and active binning regions across all your images. The first 2 of these are particularly important, though for best results you also want the same active binning region. When I use BASS I have all the images loaded, so I can apply the same identical corrections to all images in one go, rather than process the calibration, standard star and target star images separately. Noting this easiest performed on the stacked calibration, standard star and target star images rather than all the individual sub-exposures.
Also, just to check you are not really drawing the response/continuum curve freehand. With BASS you select points in the raw response profile that avoid absorption/emission lines, or any other nasty sharp features, so you get a nice smooth curve.