How do you know they're uniformly not caused by discrimination?

Various studies indicate a roughly 20% longer sentence for black men than white men given the same crime. (Exact numbers vary depending on study and type of crime, but it's somewhere in the ballpark.) This kind of thing is widely used as an example of systemic racism.

That is, it's considered to be evidence of discrimination.

Given that the corresponding number for women and men is at least twice as large, how can that not be discrimination?

Presumably some of the problems aren't discrimination, but you could be more precise in distinguishing what you are referring to, because when many problems are together in a big "X is not fine" pile, different parts of the pile may have different causes.