Scotland were cruising at half-time thanks to a Jordan Rhodes double but Lars Gerson's well-executed free-kick 90 seconds after the restart changed the complexion of the friendly. Scotland suffered some nervy moments and struggled to maintain their cutting edge, although Rhodes had another goal disallowed, but Fletcher felt Swiss referee Cyril Zimmerman had an undue influence on proceedings.
"The first half was a very good performance," the midfielder said. "The second half, the early goal really gave them a lot of confidence, the pitch started cutting up and they started kicking a few as well and the ref wasn't giving yellow cards."
He added: "So it turned into a real nasty and hard second half but we dug in deep and saw out the match and got the win that we came here for. Some of the challenges were quite bad and in friendlies it's not what you are wanting. And when referees are not going to give yellow cards, they are going to keep doing it.
"But that was the challenge that was set in front of us and the players dug in deep and kept going and didn't let it affect them. They knew they were going to get kicked and not much was going to be happening about it but they were still brave and went in for the challenges. Fortunately no-one got injured but after a few of the challenges that went in, I think we were quite lucky in that respect."
Caretaker manager Billy Stark admitted his disappointment at the second-half display, although he praised Luxembourg for their response to Gerson's impressive strike. But he felt victory was the main aim after Scotland's poor start to their World Cup campaign, which leaves them with two points from four games, and Fletcher agreed.
And the Manchester United midfielder felt the continuing emergence of Rhodes and the introduction of new caps Andrew Shinnie, Leigh Griffiths and Murray Davidson made it a worthwhile exercise.
"The win was the most important thing, on the back of not winning for a while," Fletcher said. "The longer you don't win it's disappointing. Also the young lads, Jordan scoring two goals, and the way all the young lads came in and applied themselves and performed well, I think they are the highlights to take from it."
Rhodes was denied a hat-trick by an offside flag and now has three goals in two international starts.
"He's a goalscorer first and foremost," Fletcher said. "The second goal ricochets a little bit in the box and it falls to him. He's got that real striker's instinct. And he's a real good lad, a pleasure to have around the place. He's always looking to learn, he is relatively young and inexperienced at international football, but he is improving all the time."
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- Jordan Rhodes