While others pundits have basically pointed out the various loopholes of the law, allow me to try to outline what the security agencies can legally do, as opposed to what they have been doing all along, within the confines of Human Security Act of 2007.
One very glaring loophole of the law is its provision for compensation of P500,000.00 pesos for everyday that an accused has been held in detention for charges of terrorism if he is subsequently acquitted. Take note that nowhere in the law does it state that to be entitled to compensation, he must have been wrongfully accused. Thus, under the law a person who was acquitted for failure of the prosecution to prove guilt beyond reasonable doubt may be entitled to compensation. The law provides:
SEC. 50. Damages for Unproven Charge of Terrorism. – Upon acquittal, any person who is accused of terrorism shall be entitled to the payment of damages in the amount of Five Hundred Thousand Pesos (P500,000.00) for every day that he or she has been detained or deprived of liberty or arrested without a warrant as a result of such an accusation...
Ordinarily, to be entitled for damages for malicious prosecution, there must be a separate judicial proceeding to determine whether indeed there was malicious prosecution. And it is not the government that would shoulder the compensation, it would be the government officials who are deemed to have acted beyond their powers who shall be liable.
Thus, the law shortcircuits its intent both ways: government agents acting in good faith to stop terrorists would hesitate from applying its provisions and stupid government agents can be gung-ho with it because they won't be paying the compensation after all.
Taking this into consideration, government agencies led by a person in his right mind will not file any charges of terrorism unless they are sure that they can get a conviction. As in everything that enters the courts, there is no such thing as an open-and-shut case.
How should they go about it then?
Use its provisions for investigation and the gathering of evidence. Then, file a case under the Revised Penal Code or special law, not under the anti-terrorism law. For example, murder or multiple murder, as the case maybe. In the long run, what's the difference between 40 years and reclusion perpetua anyway?
What then is the use of the anti-terrorism law? Just a justification for the enumerated powers for our national security agencies. Not that they have not been doing these things anyway.