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 is also some disagreement as to whether guitarist Robbie Robertson was present at the February recording sessions, or, 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. There is no mention of Robertson in Krogsgaard's documentation of the personnel for the February sessions. Daryl Sanders, in his account of the sessions for Nashville Scene in 2011, makes no mention of Robertson in relation to the February dates but says: "When he returned in early March during another short break in his tour, he brought The Band's guitarist Robbie Robertson, who added a blues flavor to the six-string mix." And Barney Hoskyns, in his book about The Band, Across The Great Divide, says “Even Robbie took a backseat to guitarists Joe South and Wayne Moss, waiting till Dylan returned to the studio in early March to add his distinctively ratchety licks to the gritty blues of ‘Obviously 5 Believers’." Finally, Charlie McCoy, in an interview for Hit Parader, October 1966, said that “The second time Dylan came in he brought his own guitar player with him - Robby Robertson - who by the way is one of the best blues guitar players I've ever heard in my life.”
Robertson himself, in his 2016 autobiography Testimony, while seeming at times to betray a somewhat shaky memory of events 50 years in the past, 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.
All this, of course, raises the question of who played the unforgettable lead guitar part on "Visions Of Johanna", recorded on the first day of the February sessions. It has always been widely assumed to be Robertson, and indeed for many listeners the sound of these lead guitar phrases has probably formed part their mental map of Robertson's style. Daryl Sanders, in the article referred to above, states that the lead guitar was played by Nashville guitarist Wayne Moss, apparently on the basis of an interview with keyboard player Bill Aikins.* But that lead guitar still sounds undeniably like Robertson, and he is indeed credited with it in the documentation for The Cutting Edge 1965-1966, Collector's Edition.
Evidence of a probable explanation is provided by the 2003 SACD 5.1 surround mix of the album. On "Visions Of Johanna", the front centre channel apparently presents just what was recorded through Dylan's vocal microphone, i.e. principally his voice and harmonica. (His acoustic guitar was mixed to a separate track on the 4-track tape, along with the bass guitar; this could already be deduced from the fact that on the original US stereo album, the acoustic guitar and bass are presented on the left-hand side, while Dylan's voice and harmonica are mixed to the centre.) But because Dylan always recorded his vocals live, his vocal microphone also picked up a certain amount of sound from other instruments - and not just from his own acoustic guitar. This is not surprising, given that Bob Johnston and a security guard at the studios had removed all the baffles that isolated the players from each other both acoustically and visually.† What is surprising, however, is that while all the other instruments (drums, bass, acoustic guitar, electric rhythm guitar and organ) can be heard, at least faintly, leaking onto this vocal channel, there is not a trace of the lead guitar; nor is there any trace of the cymbal strokes played between the verses of the song, which have always accompanied the lead guitar in the various released stereo mixes. This very strongly suggests that the lead guitar and cymbal were not recorded live, but were dubbed onto the spare 4th tape track at a later time. Given the quantity of other evidence indicating that Robertson was not even present at the February sessions, this was most likely done at the second group of sessions in March, when Robertson was documented as present and indeed played on several other songs. Michael Krogsgaard reported that he could not find any detailed list of takes for the March sessions; if he had, then we might have learned about this overdub when he published his research back in 1995.
* Aikins was documented as being present at the session, but does not seem to have actually played on any of the songs recorded.
† See both the Daryl Sanders article referred to above and Greil Marcus's 2007 article on the sessions for Oxford American.