Hi Erik,
Which tutorial was that? Did you use BatchPreprocessing or did you do the individual steps to integrate the bias frames to create a master bias, calibrate the darks, integrate the calibrated darks to create a master dark, etc?
I can't think of anything obvious that might have gone wrong but it's always possible
Could be something to do with the pedestal on the FITS files. It's also possible that your result is OK and something weird has happened with the screen stretch.
I'd start by looking at your bias and dark masters to see if they look reasonable on visual inspection and then check them with the Statistics process to see if the data values look sensible too.
If you don't mind uploading a few bias, dark and light frames and the masters I'd be happy to take a look at them.
Cheers,
Rick.