They could be puddles but it looks like something bleeding thru the runway.
They looks like puddles to me, and I don't see any bleeding. Do you see something different compared to my screenshot ?
What about the rain disappearing between the takeoff end of 31L and Gate 39?
I don't see any problem there too or anywhere else, you might simply have come across an dry area between two puddles, and thought the rain disappeared, probably because you are accustomed to how the default airports looks, which is really overdone and not very real.