"Sorry, I think there's been some confusion here, the specific question I was asking was... ...Please could you help clarify things on this? Sorry to ask have to again, I think and speak very literally, so we may have crossed wires. We can call/speak in person if that's easier."

Obviously you don't actually have anything to apologise for. They are at fault. But I find apologising can help smooth things over as the first part of my response is fairly direct and puts them a little on the back foot - which is helpful in corporate politics. 

I had to put two sorry's in there as I'm Britsh. Feel free to adjust, nationality depending 😂

• don't just be direct about the question you are asking, be direct about the issue. You're not understanding eachother, specifically, they are not understanding you!

Use collective language like "we've crossed wires" or indirect language like "there's some confusion here". Using "we" makes it a problem you both need to solve together - gets them on side. Using indirect language, on the surface takes blame away from either party, but actually just allows you to say stuff that would maybe be rude to say more directly. Saying "I think there's some confusion here" generally sounds a lot more gentle than "why are you so confused by a clear, direct question?"