I'm reading a fair amount of misinformation here.
Start an app on AACOMAS and see for yourself how you categorize your coursework. You are who designates what course is a repeat of what course. There is absolutely no requirement that a course be repeated at the same school or with whatever a "transfer code" is. Transfer credits or rules are simply not relevant on a med school app.
For example: I took first semester gen chem in 1988 at a city college. I took first quarter engineering chem in 1990 or so at a state university. I took it yet again, as premed gen chem, in 2005 at a different state university. None of these courses had the same title, description, credits or course number. All three count as first term gen chem, even though I got A's twice, because I marked them as repeats of the same class, and because my categorization isn't much of a stretch. (P.S. I was pretty stupid to give away an A, see how that was not in my favor?)
I wouldn't try to "get away with" something by falsely claiming a repeat, but think about how many apps they're going through: they're not going to nickel and dime you. If you think you have a reasonable case, then claim the repeat and be ready to answer for it. Personally I think both the geology and calculus repeats are legit, because (a) it's geology, who cares and (b) first term calculus is much harder than biz calc.
Best of luck to you.