You do not fix it. It is not a problem, assuming that you process an image from a DSLR.
This caused by yourself (or BPP) having set the input hint to 'raw cfa' (which is correct for DSLR).
When the input is in a raw format, PI can find out that it is indeed in CFA format, so it is happy.
When the input is in FITS format, the 'raw' part is ignored (but does not hurt), the 'cfa' part is obeyd (and must be present for some process and do not hurt for others), but PI cannot check that the file was indeed in 'cfa' mode. This information is not in a FITS header. So it tell you:
OK, you tell me it is CFA, I believe you, but I cannot check. It just says so in a somewhat frightening tone
![Wink ;)](http://pixinsight.com/forum/Smileys/default/wink.gif)
This is about the only warning you should ignore during the preprocessing.
-bitli