Mickelson, who became the first American to play in 10 Ryder Cups, appeared to criticise Watson's approach in the wake of Europe's 16 1/2 to 11 1/2 victory at Gleneagles on Sunday.
It was a third consecutive defeat for the US, who last tasted victory under Paul Azinger at Valhalla in 2008.
Mickelson, who was left out of Saturday's play, lauded the regime of Azinger, seemingly to the detriment of the current incumbent, who surprised many by opting not to utilise the rookie pair of Jordan Spieth and Patrick Reed in Friday's foursomes.
But the 65-year-old brushed aside any speculation about a problem between the pair.
"The issue between Phil and myself is basically a difference of opinion," he told Sky Sports News.
"He has a difference of opinion where he would like to manage the team and I certainly had my own opinion on how I'd manage the team.
"That's the controversy and that's the issue but I have to say that I'm very proud of my team's efforts. One thing I asked them to do from the beginning was to give absolutely they have and they did. They just ran up against a buzz saw.
"The European team was very strong and had four of the top five players in the world. When you play against them, you better be firing on all cylinders and frankly, we weren't so that's it."
Azinger led the US to a comprehensive victory six years ago having employed a 'pod' system, dividing the team into three groups of four players who featured alongside each other in the foursomes and fourball formats.