Another option, rather than have 1 procedure for handling non-conformance, you could integrate how you handle it depending on where it arises. e.g. if you have a goods in procedure which defines how product is received and handled, add the bit about how you deal with it when is wrong as well as when it is right.
Then do the same for the manufacturing area etc. In other words, build it into each process - I often find it more natural than having to go to a different procedure and it is also easier if you have different actions depending on where the problem arises.