Here's the thing. The government is not one monolithic entity. Not everyone knows everything that goes on. Which is perfect for maintaining secrecy. When your research lab is working on a secret project and it accidentally gets sighted by some dip shit Air Force flunkie working as a guard in some shack on an abandoned base, and he reports it as a UFO and then the investigative branch of the Air Force doesn't know what's going on and reports it as a UFO, the research branch is probably beside themselves with joy. "It's okay lads, they don't know what it was. And get this, the public think it was aliens! Lol!"

What's the perfect cover for your research project being spotted? It was fucking aliens, man! Aliens! Dipshits. Of COURSE they're going to release their UFO reports. It's misdirection.