how to get rid of white lines between lines and fills when saved into pdf

Is this Live paint?

It gets automatically expanded when exporting to PDF. 

Those look like 2 different blacks. Is that correct?

What's happening here: that is an antialiasing issue. It will most probably not print (but can still happen on some desktop printers or in Large Format - depends on the RIP).

To prevent that you would have to stack shapes that at least slightly overlap.