Well it's been explained (sort of). What I wasn't taking into account is that any card purchases made at the weekend won't get posted on my statement until Monday. So If I shop at Whole Foods on Monday as well, it'll appear that multiple charges have been made on that day. Going back through my statements from the first instance of this I could find (from the earliest statement I can access online), it appears that the vast majority of these multiple charges have been made on Mondays. And also discounting multiple charges on Tuesdays on weeks in which the Monday was a Federal holiday, I can only find 4 other instances of double charges, and these occurred on Tues, Wed and Fri. They all happened over a year ago and I'm not sure I have the inclination to investigate whether or not I made two trips to Whole Foods on those days. It's unlikely because my schedule only allows for one shopping trip a day, but I'm not confident about it enough to risk sitting in a Whole Foods security office seeing camera footage of myself making two trips (provided they even have footage going back that far).
Don't know why the weekend thing didn't occur to me - I guess I never really pay that much attention to dates when I skim over my checking account. It's funny but I go over my business account with a fine tooth comb every week, but my checking account not so much. I've even stopped paying attention to things like utility bills, phone, internet etc. This is what happens when bills come out of your account automatically, you get complacent....