It has been bubbling under the surface for a while. Maybe no one wanted to fully admit that the same young men who went to the frontline and defeated - with the help of NATO - the firepower of Muammar Gaddafi, are now a source of instability in the new Libya. They were regarded as heroes, but now they are merely militiamen who act with total impunity.
Libyans are fed up and once again it was Benghazi that took to the streets chanting "no, no to the brigades". Faced with popular anger, the government ordered the disbanding of illegal militias, meaning those that do not fall under the command of the defence or interior ministries.
It's a knee jerk reaction that could have even worse consequences. Indeed, some bases have already been evacuated, but where did the former rebels go? And where did they put their weapons? And will they really just go home and become peaceful civilians?
Apart from ordering them to disband, the government has not offered an alternative yet. "They will go underground and who knows how they will re-appear. I would advise everyone to take care," said Fathy Baja, a political activist and former member of the National Transition Council.
But the issue of brigades is at the heart of the political struggle in Libya. When Libya's President Mohamed al-Magarief appeared on TV he was surrounded by the most powerful field commanders in eastern Libya. These are all considered Islamists and these are the only ones considered legal. Officially they come under the command of the government, in reality they hold considerable independence and have their own chain of command. Some of them had spent time in Gaddafi's jails and were freed under an initiative orchestrated by his son Saif al-Islam Gaddafi back in 2008.
The popular anger was also directed at them. People were clearly demanding for all the brigades to be disbanded and for its members to join the security forces if they wish, but on a personal basis, not as an entire battalion.
The government protected them and somehow gave them more of a legal cover. Hours after the protestors stormed the Raffalah al-Sahati brigade, men dressed in official army uniforms were seen entering the base. The national army was apparently taking over. The sign was changed - now it states that these are the Shield Forces of the defence minister. For many these are cosmetic changes. Many say that what is happening is that Islamists - and even extremists - have their own military power within what's supposed to be a national protection force.
It has been the question since the beginning of the revolution. Are extremists leading the fight? Gaddafi had repeated it over and over again, but everyone dismissed what the defunct leader had to say. Now his words are coming back to haunt some Libyans.
Islamists have emerged as the most organised and powerful force in Libya. They rule and are gradullay imposing their will. Many Libyans are left wonder what will be the consequences as Libya prepares to write its new constitution. Islamists say they will accept nothing short of the total application of Sharia. Many Libyans say they don't need Islamists to rule them but technocrats. They say contrary to Egypt and Tunisia, Libyans are already living a conservative life. What they need are experienced people who know how to build a country.