Spelling and typing mistakes. Please ask someone who pays attention to detail to proof-read your site. When one credit card merchant launched its program the site looked beautifully professional - but was spoilt by glaring typing mistakes in the first few sentences on the main page. If you don't want the link to your affiliate program to be obvious to your main customers, that's fair enough. However, if you do want webmasters to find the link, make sure it exists.
Some people forget.
No FAQ page. As well as your main FAQ, it's an excellent idea to have another list of frequently asked questions for affiliates. They will wonder what you have to hide. No privacy statement. Your affiliates have a right to know.