It's not what they did. It's what they didn't do. They didn't maintain a chain of custody over the machines by the election officials in charge of them.
To put it into simple terms. It's like having a handgun that you make sure is unloaded. You lend it to a friend, and when you get it back you can no longer treat it as unloaded.
The election equipment was certified to give absolutely accurate tabulation. When they get it back, they have no idea if the auditors put a bullet in the chamber (bug in the software).
That's why all the machines need to be either re-certified, a lengthy expensive process. Or replaced with certified equipment.