I believe I have two small (2") areas in my new shower pan where the wall meets the floor that don't drain properly. The rest of the shower floor drys overnight and is dry by the next morning after the previous days showers. These two areas are visibly wet and just won't dry. I sloped the concrete subfloor, laid the pan liner down, sloped the next layer of cement while keeping the weep holes open with pea gravel, and then laid tile. The only thing I can think of is there may be a wrinkle in my pan liner that is keeping the water in that corner where the wall meets the floor. How do I fix it or do I need to worry about anything except mildew and mold?

Mildew or mold may become a problem but less if the shower is used daily. Hit it with mildecide or bleach once and a while. There could be a wrinkle but I suspect that your corner tile is too low compaired to those around it. Test it for level with a straight edge to see if the tile dips. If the corner is low you need to pop those tiles and build up with mortar or modified thinset.

No, the tile isn't lower, cause water doesn't pool there, it soaks into the grout and stays there. It just seems like it won't flow away under the tile like the rest of the shower does.

Water should not be able to soak into grout. The water is standing on the grout and not draining due to a poor slope. No water should be under the tile if you grouted properly. Have you tried the straight edge yet? It must be lower or at lease not sloped.

No, the tile isnt lower, cause water doesnt pool there, it soaks into the grout and stays there. It just seems like it wont flow away under the tile like the rest of the shower does.

Did you seal the tile and grout properly before you began using it?