I don't think it was a mistake. How much difference is there between 75 pitches and 120 pitches when it comes to how long it takes to rest up? And with the bullpen being used heavily on Tuesday, they needed the rest.
I've also heard a lot of analysts sayint that with the way Prior pitches with his legs, it doesn't put that much strain on his arm - so I think he could go on 3 days rest easier than a lot of guys.