I hate, Hate, HATE it when the Oxford comma is not used! In my mind, it is never acceptable not to use it. I think the final comma was first dropped to save ink when printing but come on! You can't save that much money. Just use the comma, please. APA requires it.
I looked this up for my dad once in my APA manual and there are times when punctuation should be inside quotes, and times when it should be outside of the quotes. Your usage was correct and I totally agree with you about the internal logic of the material.