I think it's very unlikely there's real money in it. Most likely it's "real-ish" bills taken early from the production line without any of the security features, if not outright prop money - it's not like someone can inspect the printing or security features through the glass anyway. There's little upside in using real money, and plenty of downside.
Let's say the cube gets damaged and needs to go for a repair or rebuild - real money would require emptying it under supervision and counting the bills, where as fake money can just be sent as-is to the contractor, and any visible shortfall can be made up with more fake money upon return if needed).
Those downsides don't seem that bad to me. If something needed repair, they can bring a contractor on site, and certainly the Fed has cameras and police to monitor.
(In line with some other commenters, I'm more inclined to believe it's bills they've taken out of circulation than "almost finished" ones -- security features are built in throughout the process, not just an extra step at the end.)
Cameras still need to be monitored which costs money. Plus sleight-of-hand and other tricks are a thing, so you'd probably still need to background-check any contractors and maintain a strict chain of custody over access to the cube and then recount and re-check to make sure none of the currency has been substituted by lookalike fakes. Police still costs money.
If there is no reasonable way for the public to notice, why not make everyone's life easier by using fake money? That would be easier and cheaper.
Leaks can be dealt with by the legal system (pay people decently and make them sign an NDA in exchange not to disclose the bills are fake) which is much easier than actually keeping track of 1M of currency.
Let's say the cube gets damaged and needs to go for a repair or rebuild - real money would require emptying it under supervision and counting the bills, where as fake money can just be sent as-is to the contractor, and any visible shortfall can be made up with more fake money upon return if needed).