How is air getting into my lines?

You talking to me?
You talking to ME? :D

I have had master cylinders return from a pump and suck air in around the cups before the piston seal in the master cleared the return port.

On ones that are being a pain I sometimes use a squeeze bottle with a plastic hose on it to fill it from the wheel cylinder up instead of from the master down.

Me too, but in that case the air would be transferred to both right and left of whichever side of the M/C was sucking air.