What causes bubbles in the master cylinder

What is your question?

Brakes got spongy and then went completely out. The left rear wheel cylinder was leaking fluid. Replaced the wheel cylinder, still no breaks. Once i use a break vacuum pump to pull the air out of the lines, had breaks for minute now no breaks. But notice bubbles coming up in the Reservoir. What can be the problems causing the bubbles in may not having no brakes?