I just finished reading Why Homer Matters by Adam Nicholson, and there was a very brief section about copies our current version was made from, discoveries of older manuscripts, and citations in authors from antiquity that differ from the version compiled in Alexandria. I would love to read more about this and the transmission of other classics, but haven't had much luck finding anything. Any help would be appreciated!
I would recommend the 'Cambridge Companion to Renaissance Humanism', specifically chapter 2, written by Michael Reeve. He goes into a lot of detail concerning problems with modern day copies of classical texts, including alterations and notes made in the margins by subsequent scholars which have become incorporated as part of the text. He specifically cites Petrach's attention to 'Pro Archia', a speech by Cicero given in defence of a Greek poet, Archias, whose citizenship had been challenged. A good read.