I've heard the claim that elements of the military have staged bombings to frame the terrorists. The problem is that both sides play dirty. The insurgent / terrorist groups could claim that to distract attention from themselves. The military could sponsor attacks to make the insurgents look bad. Both are plausible. My gut feeling with this is that the military is innocent of this, or if so, it was done by an actual rogue group.
Most of the 'militia' type groups, such as the Guardians of Mindinao, would never support attacks on their own people, even to make the enemy look bad.