Unlike in the Office Space movie it was more than just moving a few cents around. He employee ordered over 1000 items in a month (to resell?). That should ring any alarm bell already.
It didn't ring alarm bells because people were aware that he was placing "test orders". They just weren't aware that he was not in fact cancelling said orders.
In the Office Space movie, a bug in the the software they uploaded caused it to steal much faster than it was supposed to. Which led to everyone involved panicking about getting caught.
The stuff he ordered was part of a different thing than the 'Office Space' scam they also found. It was either an actual screw-up on his part, that he tried to cover up by reversing the charges, or a scam closer to the one a Microsoft employee tried to pull off a while back.