One of these generally revolves around how to handle screens or cutters through the middle of the match-up defense. Each type of match-up may have different rules. Man offenses don't work well either because of the switching defenders. Team's that don't conceptually understand how to attack match-up defenses have considerable trouble getting any offensive rhythm or good looks at the basket thus their increasing popularity. The weaknesses of the match-up are two headed so to speak.
Many teams play the match-up because they are neither a good man or zone team.
They attempt to hide weak defenders by confusing the offensive attack. This can be a benefit for sure. The match-up defense is also more susceptible to hard penetration and can only be effective if the defensive team is fundamentally sound. It is my opinion that the Match-up Defense is a great defense when well understood and executed by the defensive team. However, the learning curve for almost any offensive or defensive team tactic is steep for complex rules and adjustments.