Okay, I'm not sure how accurate this is but here goes:
Some people use the term to just describe queer people in a story, but I don't think that is really what it means, because a queer person just existing isn't really a theme.
I think a queer theme is, to put it simply: elements of a work that represent or at least mirror experiences common in the queer community. elements that can range from coming out and same sex crushes/relationships, to just ideas like found family and nonconforming gender expression. This is why the phrase can pop up in relation to works that don't actually have any explicitly queer elements. Hope this is accurate! (oh, also a theme usually don't take up the entirety of a work, so a story entirely about the queer element may not get the phrase used around it as much.)