When importing transcripts (via 'import rows') for a video, I'm frequently given an error message "rows should have the same number of commas", with a line number, and when I check the .txt file (CSV file with the extension changed to txt, as for some reason Nvivo won't recognise the CSV extension) at that line number, and the transcript does have a comma, but there are quotation marks around the text in that case. The Nvivo documentation I've read says commas will be ignored in quotation marks (with the "Dallas, Texas" example).
FYI - I have been capturing the auto-generated YouTube transcripts with a Chrome plugin, saving as .CSV files, then manually or batch renaming the extensions, then importing them. Most work fine, but I think that's because most don't have commas.