I think I do some of the same thing. I notice it more when I'm reading, actually—when I mentally have things or, more often, people arranged a certain way and then have to change it because a detail comes up that makes it clear I've got things wrong (Sherlock wouldn't be taking John's pulse from his left wrist if he were on John's right, ugh! Or I thought Mycroft was on the other side of that chair, so how did Sherlock get in his face so fast? Argh!)

I usually don't have to think too hard about how things look when I'm creating them.

What gives me trouble are sets where I can see part and can't work out the rest! Sherlock does seem to have a bathroom attached to his room, but we don't see that until s2, so I spent s1 wondering where the heck the bathroom was. (I have a toilet obsession. Have to know where it is just in case I need it, you know?) Then I've spent the time since wondering how on earth that bathroom could fit there! In fact, you gave me this link, but that's a flat plan that doesn't make a whole lot of sense. I have a bit of a draft Sherlock fic, but mostly I don't have to deal with it too much because I don't write fic for that fandom (though I read oodles of it). No, it was Primeval that gave me the worst trouble. Stephen's flat? It really, really doesn't make sense.