I'm mainly speaking of our existence, but there seems to be other things that science can't exactly tell us why they are the way they are.
Answer on Why is it that science can tell us how but it can't tell us why?
I think it's because "why" is a human description. There's no objective measure of it, only explanations from a human frame of reference (and those explanations vary wildly from person to person). Science, on the other hand, strives to reduce human error, bias, and subjectivity as much as possible - it's science's greatest strength, but it also limits what sorts of questions it can answer.