According to Catholic teaching, where does the disorder stem from? According to the Catechism of the Catholic Church,  


  homosexual acts as acts of grave depravity, tradition has always
  declared that "homosexual acts are intrinsically disordered." They are contrary to the natural law [cf. CCC 2357], and the inclination to homosexual tendencies is objectively disordered [cf. CCC 2358].


This disorder, as the Church terms it, is not limited only to homosexuality. For example, the disorder in man, that say, leads to discord to the marriage union.

One comment in this article said,


  My "natural action" has ALWAYS been homosexual [...]


Noting that to the online commenter, the inclination is "natural" to them, based on her faith, from where does the Church teach the disorder(s) in man comes from?

The answer will also define what "intrinsically disordered" means.



Related: Does God create some people Heterosexual and others Homosexual? [closed] | C.SE.
As far as I know, the Catholic Church hasn't made any statement about the origins of homosexuality.

The best way to understand this perspective of homosexuality as a "disorder" is as a mental or emotional disorder.

To be clear, the Catholic Church hasn't actually called it that, but that is similar to how it has been described, both in your quoted material and elsewhere.

There are a lot of disorders: anorexia, OCD, schizophrenia, alchoholism, pornography addiction, bipolar disorder, etc. Identifying a single "source" would be complex and difficult. Genetics, environment, and individual choices all contribute. But regardless of the origin, these are all out of place, and we should see help from therapists, family, friends, and Christ to overcome them.

As for intrinsic, Merriam-Webster defines it as "belonging to the essential nature or constitution of a thing". Thus, intrinsically disordered means inherently incorrect. Homosexuality is not conditionally or occasionally appropriate; it is incorrect in and of itself.

Your quote also says that homosexual tendencies are objectively disordered, which means it is wrong even from an impartial viewpoint. Put those together, and Catholicism sees homosexuality as fundamentally and clearly out of place.