Tiny air bubbles are still compressible. And, don't move very quickly through fluid. They will eventually collect at high points of the system. Hopefully the physical arrangement on your bike makes the master cylinder the highest point in your brake system. If so, they will self bleed in time. If you were flailing on the brake handle to pump up the pressure, you can be sure that the fluid became foamy and high internal pressures can make large bubbles into very slow moving tiny ones.
I find it is helpful to mentally visualize the inside of the liquid vessel. Peering inside, start at the very bottom and imagine where a tiny bubble would rise in the vessel. If you can make it move toward your speed bleeder so much the better. If there is a line loop or shelf that can prevent a bubble from rising to the master cylinder, that's your problem. Sometimes you can reposition bars or bike to eliminate the capture pockets, and that allows the bubbles to rise with time to the master. Then a slow pump on the handle squeezes out the air, and the brakes get a hard lever.
The other factor could be new pads that have not worn to the point of full contact with the rotors. Inspect those and note how much of the puck surface is showing wear factors. If the surface contact is full, flat, and complete, spongy levers are probably bleed issues.
Cheers,