It's bad luck, as well as perception/confirmation bias.
Use Poe, he blows those things out of the sky. Assists also work well, since they double the chances of someone hitting. Each flagship has a way of taking it down, which generally boils down to ignoring it: Endurance target locks it somehow (TIE Advance, 5s, etc) and then takes it out with its AoE. Executrix waits until Imperial Assault is available. Chimaera waits until its atuo-kill is available. Home One is the only one that really actively goes after it, using its basic (and the AoE once you have some buffed ships) to just overwhelm it with attacks. Alternatively, with Home One you can wait until Master Plan comes up and then use Poe's special back to back.