Triple Rep (2x Complex, 1x Enhanced) Madrugars are vulnerable to Large Missile Launcher fitted tanks due to the massive burst damage from missiles with a damage mod; lower buffer due to a lack of either a plate or hardener to absorb damage; and the damage bonus missiles get against armour. The Triple rep Madrugar works by drawing out fights where it's superiour sustained tank can help it keep going under constant moderate damage. But with the Large Missile Turret, there isn't enough time to get repairs going to keep the tank sustained, and thus it blows up. However, if you miss with enough missiles, the Madrugar can easily regain it's armour and then you might have some problems due to your long reload time, especially if you had to expose yourself to get the shot on the Madrugar in the first place.

Does that explain it for you?