I'm just doing my thesis corrections and, apart from a few general typos, one thing my external examiner picked up on was what he described as "inconsistency" in my quoting style; sometimes my punctuation was outside the quote marks and sometimes inside.
Now this is a little system that I thought I had invented and which I knew would probably get me into trouble. It is that, when the punctuation (usually full stops) is from the text I'm quoting it goes inside the quote marks---it's being quoted---and when it's my punctuation it goes outside the quote marks. The stylistically normal method is to put all punctuation inside the quote marks.
I was about to give in and re-format all my quotations to use the conventional style. However, I then found an interesting article by Larry Trask from 1997, then in Informatics at Sussex. He describes exactly the system I've used and describes it as the "logical view", opposing it to the "conventional view", and giving some good examples. He also cites an article by Geoffrey Pullum called Punctuation and human freedom (Natural Language and Linguistic Theory 2:4, Nov. 1984, pp. 419--425) in which Pullum describes his use of the logical view and his annoyance at copy editors insisting on re-shuffling his carefully quoted punctuation.
As a result my logical punctuation stays. That is how it will appear in the final text deposited in the library. It's a small victory.