While I am certainly not defending the IRS, be aware that it, like most large businesses, is subject to annual reviews of internal controls. It, unlike non government businesses, publishes summaries of such findings and recommendations. Regardless of the entity being audited, these summaries tend to run dozens of pages long.
The IRS, like any business that processes a substantial amount of hard copy documents, is more prone to human error than a business that is mostly electronic.
All IRS refunds are subject to subsequent audit and the IRS has three years to claw back excess payments and they do. This is no different than tax payers having 3 years to amend a prior return.
2003
U.S. GAO - Management Report: Improvements Needed in IRS's Internal Controls
2004
U.S. GAO - Management Report: Improvements Needed in IRS's Internal Controls
2005
U.S. GAO - Management Report: Improvements Needed in IRS's Internal Controls
2006
U.S. GAO - Management Report: Improvements Needed in IRS's Internal Controls
2007
U.S. GAO - Management Report: Improvements Needed in IRS's Internal Controls
2008
U.S. GAO - Management Report: Improvements Needed in IRS's Internal Controls