I've seen a lot of misuses of the word conflate lately. Many folks seem to be using it as a cooler-sounding synonym for confuse, as in "don't conflate political ambition with political knowledge."
I have to quote Inigo here: "You keep using that word. I do not think it means what you think it means." (The Princess Bride)
According to my trusty Merriam-Webster (11th edition), this is the definition of conflate:
"conflate (vt): to combine or mix (two variant readings into a single text, etc.)"
And here's the definition of confuse:
"confuse (vt): 1) to mix up; jumble together; put into disorder 2) to mix up mentally; specif. a) to bewilder, perplex b) to embarrass; disconcert c) to fail to distinguish between; mistake the identity of"
(both definitions from p. 306)
Notice the subtle (or not so subtle?) difference here. Confuse means just what everyone thinks it means. If you confuse A with B, it means you don't know the difference between them, or you think they're the same thing. Conflate, on the other hand, doesn't mean what one might expect. If you conflate A with B, it means you combine them and come up with something that's related to both, but different from either.
If you're trying to say that someone has mistaken X for Y, then you need to say that the person has confused X and Y. Use conflate only when you mean that someone has taken multiple (slightly different) statements and combined them into one.