Affiliate Marketers run into problems with merchants all the time.  The most common problems are related to money, but there are a number of things a merchant can do that will upset Affiliate Marketers:

1. Pay late (no autodeposit)
2. Reverse commissions
3. PPC policies
4. The Affiliate Network they belong to
5. Poor Affiliate Support
6. Poor Affiliate Tools
7. Change in commission levels
8. Change in tracking period
9. Double Affiliate Sales
10. Merchants who close down shop without telling their Affiliates (especially bad for PPC Affiliates)