So, if a commercial pilot does see such things, they'd be far less likely to report them, as it may well ruin their career. Navy pilots, on the other hand may well get some commendation for identifying an unusual, or anomalous thing (enemy tech?).
That aside, it could make logical sense that the military is seeing these more often for a few reasons:
- The nature of their missions, flight speed, equipment, and flexibility to investigate further
- If it’s a terrestrial adversary, it makes sense that they’d fuck with military
- If it’s ET, it makes sense that they’d pay more attention to military jets than passenger jets if it’s some kind of recon
Because they don't want to lose their job when their employer thinks they're nuts and shouldn't be flying hundreds of people.