Probably the biggest challenge we face is fixing a bug when no bug exists.
Many Sitecore installations have, for one reason or another, incompatible Sitecore dll files copied into their bin directories. These often lie dormant until they begin getting used as companies start implementing more advanced Sitecore functionality. A good example is the file, 'Sitecore.Automation.MarketingAutomation.dll'.
Incompatible files often work 90% of the time so are removed from suspicion. S4S customers with quirky issues, that may not manifest into a hard error, should check the deployed libraries to ensure compatibility.
The best tool for identifying real issues is the Sitecore log file.