Grammar Issue

One of my periphery duties at work, and main duties at DCist, is to edit. I make paper bleed left and right, all day long. There is one glaring error that I see so often that I even begin to question myself. Then I remember that it's a rule I've known since about the 3rd grade. Punctuation goes inside quotation marks. INSIDE! For example,

"Can I give you a foot rub?" Matthew McConaughey asked Amanda.
She blushed, and giggled through answering, "yes."

It's causing me to use the little transpose symbol far more often than I can comprehend. Why don't people remember elementary school? Or high school, or college, or books they read, or anything else in the world that would remind them -- punctuation goes inside quotation marks? There are exceptions to the rule (of course, because English is wildly confusing), but for the most part, keep your punctuation inside your quotation marks, if for no other reason than to ease my heartburn on the matter. Thank you.