The only time matsuri allows you to have a team less than 3 when you don't include your main in one of your lineups (you used 4 ninjas in one lineup), which leaves you with 5 ninjas and your main. If you decide to make a team with either your main + 3 ninjas or 4 ninjas yet again, the next team you can make is less than 3 unless you decide to revive. Outside from that, the system wants you to use 4.