I read in some articles that your affiliate links may be pirated so that someone is getting credit for your sales. Is it in the script or how do you find out if it is happening to your site?
I think there might be some sort of malware/virus that does this. It would basically have to hijack an infected user's browser and change any links it recognizes as CJ links (or links from another affiliate program) and change the referral ID to the virus maker's. It would work in much the same way as ad blockers do. If such a thing does exist, there's not much a website owner can do about it, since it's the users computer that's infected.
That is why it is important that you clean your computer whenever you can. Run the virus programs and such every day or at least once a week.