Meanwhile, however, Overstock had been underbilling its fulfillment partners for certain costs related to product returns over the past two years, Chidester said. "In other words, we weren't recording some customer refunds and we weren't recouping some costs from partners on some returns. The combined result was that our returns costs looked reasonable."

The company has since "reexamined [its] procedures for testing and verification of the balance sheet" and "put into place processes to record all refunds in our financial system," Chidester added.

One observer said problems like those cited by Overstock.com can happen on any ERP project without the proper care and planning.

"The ERP system will do what you design it to do, which is why we often say it's very important to spend time on design and mapping," Forrester Research analyst Ray Wang said via e-mail Monday. "Of course, it's even more challenging if this is the first ERP system put in at a company. In that case, you are challenged with capturing all manual processes."

Overstock's Moon called Wang's comments "spot on" and said Oracle has been "a great partner."