I have had brown film base color when the pH of my CD was a bit too high, but these negs were still scanable and printable. Depending on exact CD formulation, the pH of CD can go up or down as it is reused. The problem with fog (and that's what your brown film base really is) is that it is quite difficult to control, so if it is there it quickly builds up density.
You may have had a bad combo of excessive CD alkalinity and too high process temperature, and correcting either one could have saved your negs. If you don't have the means to correctly set temperature and pH of your CD, then you need to process short test clips before you process important rolls in order to verify that your process is at least roughly in spec.