Police fired teargas shells and used batons to disperse the crowd.
Protesters also burnt effigies of Banerjee and vowed to continue their fight for Gorkhaland.
Security personnel in large numbers were deployed in the hill district of West Bengal after widespread clashes between GJM activists and the police were witnessed on Saturday.
Around 2,000 Gorkha Muslims staged a protest march supporting the Gorkha Jamukti Morcha cause.
The list, which is a mix of seasoned political players and greenhorns, has 17 women candidates, five more than the last elections, constituting roughly 41 per cent of the candidates.
Barring Maharashtra, the poll percentage in rest of the states was in excess of 60 per cent while in Puducherry it was 80.47 per cent.