If the fluid was really dirty it's possible the return hole in the master cylinder got clogged preventing fluid from going down. There may or may not be a small metal cover in the bottom of the MC, under it is a very small hole, if it is clogged it will cause problems. In the future do not drain the fluid completely before adding new fluid.
Yep, check that screen. When I rebuilt my break system, rebuilt master cylinder, braded lines, new caliper seals, I used a miti vac to suck out the air in the system. I use this when flushing the clutch and breaks also. You are not the first to do this and will not be the last. Just keep and eye on that fluid level when doing any service!