How is air getting into my lines?

Technically you are not supposed to push the pedal more than it's normal braking travel, due to possibly stirring up any crap settled in the cylinder where the piston seal has never traveled and causing a leak, or leak by.
But if that happens you kind of need a new one anyway, or at the least an inspect and clean job.
I think that rule kind of came out of the retail industry so if you bled someone's brakes on a brake job there was a possibility of the customer driving off with bad or leaking brakes and end up with a come back or even a law suit.