Yes he has flaws. When discussing his record, however, it's important to point out to somebody who's acting as though his record is not that of a top manager that he's won multiple league titles in 3 different countries and has won the CL/European Cup, along with many other cups.
The flaws I see in his current United team are:
1: lack of high press. I prefer Pep's aggressive style of pressing to Van Gaal's more conservative approach of pressing from the half-way line. However it is making us defensively compact.
2: A lack of urgency with the ball. We often use the ball as part of a defensive strategy. Defending with the ball, if that makes sense.
3: Lack of movement between the lines. Van Gaal likes very structured attacks which demand a lot of robotic memorisation and practice from the players which can stunt our creativity.
My comment about our lack of a potent attacking force is, however, much more important than all three of the criticisms I make above. The reason for this is because possession football is a percentage game. The more you have the ball, the more opportunities you have to attack. Everybody knows this. But without players who can pose a consistent threat of beating a man multiple times in the space of 90 minutes, it's quite easy for teams to park the bus and watch the play endlessly switch from side to side in front of them.