It’s not necessarily some intentional conspiracy, but rather the question of care and communication, etc.
Everyone knows their IFF is dogshit. There’s a surprising regularity to airlines being shot down, even before the war.
A UAE-based airline’s planes are going to be less likely to fall through the cracks, so to speak, than an Azerbaijan-based airline’s
Part of it might also be that sometimes, military or intelligence flights might squawk ads-b with a spoofed signal to blend into the overall traffic.
It isn’t that they didn’t know they were there, it’s that they didn’t believe the ID. It’s not just the hardware that’s the problem. (The hardware is dogshit, but so are the people using it. People are part of the system, too, and they’re fairly poorly trained.)