Presumably you mean aside from the fact that we haven't seen any sign of the high energy signatures that would surely happen from annihilation collisions when the solar wind meets this interstellar anti-matter.
If you're going to question facts within fictional works, I'd start out by with the point that we didn't actually discover warp theory with the help of four thumbed aliens from Alpha Centari. After that, the properties of interstellar gas seems fairly minor.
To be clear, let me restate: I haven't seen anything directly contradicting the "interstellar hydrogen is mostly antimatter" idea within any canon work of the fictional Star Trek setting invented for television and expanded in books and films by authors who are paid to invent stories for entertainment. This statement does not imply that I believe or have proposed any sort of belief that the vaguely defined warp drive, humanoid aliens, Q Continuum, transporters, tribbles, or an English actor playing a French captain are actually realistic nor exist in the real world. Well, the bit about the actor is technically true, but otherwise, it isn't real.