If you did not get the wire retaining spring clips properly back in place, you will have a low pedal.
It is also possible to damage the master cylinder if you pushed the piston calipers back too quickly. I make it a point to open the bleed ports when I push the pistons in so that I do not force dirty fluid backward in the system. If the fluid is dirty enough and you push the piston back too quickly, you can collapse the cups in the master cylinder. If you do, you need to either rebuild or replace the master cylinder.
Check the retaining spring clips first, then bleed the entire system again to make sure that there is no remaining air. If neither of these things solve your problem, you will probably need to replace the master cylinder.