MIT uses NDAs and non-disparage agreements to cover up research fraud. It's not uncommon.
I was intimidated into signed an NDA which says I can't talk about the NDA. The threats were serious, and I don't talk about that NDA.
Unless you're at senior levels of your university, you wouldn't know about sketchy stuff like this going on.
The way to solve this would be to extend restrictions on federal grant funding and financial aid to only encompass institutions which don't use tools like this.