Like you said earlier - you never know why a person orders what they order; could be anything - preference, allergy, etc. Since I rarely order coffee or anything like that, I don't have to be super vigilant with watching..but I was trained as a young kid to go through food orders when I got them at the table - my dad's allergic to cheese and so we always ordered without cheese. Similarly, I do not prefer tomatoes and if a dish comes with them when I've ordered it without, I make it really clear that simply taking the tomatoes off will not cut it -- and if whoever in the back does it, the manager hears about it.

How is it that assholes seem to be in the jobs that most require customer service and compassion? (yourself excluded, of course) - by and large it seems like there are so many more jerks in roles like that than nice, understanding people. I know that you've been frustrated by customers (biscotti lady, for example), but I know that you would NEVER be careless with an order or give lip about it.