United had 80% possession and enjoyed plenty of shots at Boaz Myhill's goal, but the Welshman was in great form, and the home side were unable to find the breakthrough meaning they lost at Old Trafford for the third time this season - the worst in the top four.
On Match of the Day, Neville questioned why the United boss adopted a second-half formation that had many individuals operating in positions they would rather not be playing in.
"In any team you have one or two players out of position but in the second half Manchester United had four or five players out of position and that's why they didn't have any flow," the former Everton captain said to the BBC.
"They had two wingers (Valencia and Young) at full-back, two centre-forwards (Rooney and Van Persie) in deep midfield and a midfielder in Fellaini as a centre-forward. That's too many players out of their best position.
"Manchester United have given Liverpool a glimmer of hope of finishing in the top four and they need to shape up."
Neville could have arguably picked further players who weren't playing in their natural position. Ander Herrera isn't best suited as a holding midfielder, but the fact Van Gaal went with two of the Premier League's best ever strikers in an attacking midfield position was a peculiar method in trying to get back into the game. Valencia has of course played fullback much of this season, with Young also trying his hand at fullback to a reasonable standard when necessity demanded it, but five players out of position was too much for the 38-year-old.
The former England man was a versatile player himself, capable of putting in adept performances in a variety of defensive and midfield roles, but he clearly took issue with the fact that Van Gaal was so prepared to play so many players out of position.
The Dutchman comes from a culture that invented Total Football, the idea that any player can fill in for one of their teammates regardless of their preferred position, but this is something that hasn't always worked out during his time at Old Trafford, and may hint at further redevelopment of the United squad comes the summer.