Some people have suggested that the 92 magazine presents rounds from a feed angle that would not be optimal for a tilt-barrel design. I'm not a gunsmith, so I can't say anything about whether or not that's true, but it seems plausible.
The tilt-barrel/short recoil Walther PPQ and P99 use a magazine that is practically identical to that of the Beretta 92FS (aside from the location of the mag catch hole and the baseplate details), and they feed just fine.
In fact, a Beretta 92 mag functions flawlessly in a P99 if you drill a new mag catch hole in it.
Beretta could have easily made 92 mags work with this new pistol if they wanted to. We all know why they didn't.