Somewhat offtopic, but why do affiliate programs go along with this? If it's a link that was already going to Amazon, then adding the tag brought in no new business and CloudFront does not deserve a cut.
You mean CloudFlare. CloudFront is Amazon's CDN service :-)
For Amazon at least, intercepting and tagging URLs is in violation of the Associates agreement, and if detected Amazon will not pay these fraudulent commission claims.
If the URLs are being tagged with the Associates account of the web page owner, then this auto-tagging is a CMS feature, which is reasonable.
If the URLs being tagged are content created by NOT the website owners (like, say, forum posts), then we might be back in fraud territory.