The protest, which targeted the UN convoy near Goma's airport, was one of several demonstrations demanding an extension of the security zone.
Protesters are angry that a new UN security zone will not take in the regions under the control of the rebel M23 movement, which briefly controlled Goma in November.
N'senga's Fight for Change (Lucha) youth movement issued a written statement that called for the immediate extension of the security zone "in order to secure thousands of other civilians who are in zones under the occupation of the M23 and other armed groups".
The M23 rebels briefly controlled Goma in November, and subsequent peace talks with the government have repeatedly stalled.
UN peacekeepers began patrolling a new security zone in the Goma-Sake region on Thursday.
The area has about a million residents and includes dozens of roving militias.
"It is absurd to claim to protect the civilian population 'in densely populated Goma and Sake' without protecting the sources of food supplies which are currently in the regions plagued by armed groups" in Nord Kivu province," the Lucha statement said.
The group has accused the M23 rebels in recent weeks of looting, kidnapping and other attacks on civilians.
The commander of the UN force, Brazilian General Carlos Alberto Dos Santos Cruz, said that the parameters of the security zone were not fixed.
"This is only a first step. Each zone has its own particular conditions," he said.
"We are going to adapt to the situation on the ground."
The security zone was established after the UN Organisation Stabilisation Mission in the Democratic Republic of the Congo (MONUSCO) gave a 48-hour deadline on Tuesday to armed groups and individuals to surrender or risk being disarmed by force.
As the deadline came and went it was unclear how many fighters had heeded the call, which the M23 had dismissed as irrelevant.
A photographer for AFP news agency saw a group of Goma motorcyclists on Thursday, honking their horns and shouting, "We are chasing MONUSCO," as the UN mission in DR Congo is known.
Goma leader Jean-Mobert N'senga said that the incident forced the shops in the area to close.
Lambert Mende, Government spokesman, said that he understood the frustration of Goma residents, but that the government and UN peacekeepers were trying tofind a solution to the crisis.
The UN gave no immediate indication that military action had started or was planned in the troubled region which holds massive potential mineral wealth for a country that is almost as big as western Europe.
DRC has been wracked by violence and civil war since independence from Belgium in 1960, often rooted in its vast mineral wealth and drawing in its neighbours, particularly in the eastern provinces.
A statement signed Saturday by M23 president Bertrand Bisimwa said that if the government does not respect its vow to hold talks, which have repeatedly stalled, rebel fighters could be redeployed to the same positions they held last November when insurgents briefly captured Goma.
Fighting between rebels and Congo's army resumed last month after a period of calm. Last week, the United Nations peacekeeping mission announced plans to disarm anyone outside the security forces in and around Goma, where it said M23 has attacked army positions since mid-May.