Two controversies regarding the recording sessions:
1. Organist Al Kooper has repeatedly insisted in interviews that the Nashville recordings were completed within a single set of sessions spread over a week to ten days. He says he recalls making only one trip to Nashville, and that the claims of a second series of dates must have arisen from latter-day amateur researchers not understanding the studio logs. For example, an entry for an engineer running off an acetate of one of the songs could have been misinterpreted as a recording session.
It is difficult to understand how two trips from New York to Nashville could have been conflated in Kooper's memory into a single trip (or alternatively how a single trip of nearly a month could be remembered as lasting only a week to ten days). Nonetheless, plenty of other evidence does support the notion of two separate sets of sessions.
2. There has also been some disagreement as to whether guitarist Robbie Robertson was present at the February recording sessions, and, if he was present, whether he actually played on any of the recordings made. According to Al Kooper, Robertson was in Nashville the whole time Kooper was there; but, as seen above, Kooper seems to have merged the two sets of dates in his memory. Robertson himself, in his 2016 autobiography Testimony, makes a convincing case that (1) there were indeed two sets of recording dates in Nashville, and (2) that he was not present at the first set. Indeed, back in 1966, Charlie McCoy had said in an interview for the October edition of Hit Parader that “The second time Dylan came in he brought his own guitar player with him - Robby Robertson.” There is furthermore no mention of Robertson in Michael Krogsgaard's 1995 documentation of the personnel for the February sessions.* Robertson's absence from the first set of sessions has now been confirmed by Daryl Sanders' 2018 book on Blonde on Blonde., which cites further clear recollections on the matter from Robertson.† Sanders also clears up another mystery regarding Robertson's involvement: the matter of who played the lead guitar on "Visions Of Johanna", recorded on the first night of the February sessions. Most Dylan fans had always taken this to be a prima facie example of Robbie Robertson's distinctive playing style, and therefore evidence that he was in fact at the February sessions. However, Daryl Sanders tells us that the guitar part was in fact played by Nashville session guitarist Jerry Kennedy, who happened to have arrived at the studio in time to play on this song. So this now appears to be a closed case: Robertson was not there.
† That Thin, Wild Mercury Sound: Dylan, Nashville and the Making of Blonde on Blonde, Chicago Review Press, 2018, pp.127-128