Almost 500 pallets had been removed from underneath the flyover where they were being stored last week by the Department for Infrastructure with protection provided by the Police Service of Northern Ireland (PSNI).
There were later some minor disturbances which police suggested may be linked in part to the removal of the pallets.
A Department for Infrastructure spokesperson said the “illegal storage” of the pallets under the flyover posed a “significant fire safety risk” as there were gas mains under the tarmac.
The Lecky Road was closed for a time following the initial removal of the materials, with police saying some items had been set on fire on the road.
It closed again later on Wednesday night when police said pallets and a mattress were set alight on the flyover, while a motorbike was also seen to be on fire. A petrol bomb had also been thrown at police officers in Bishop Street.
First Minister O’Neill said it was “right and proper” to remove the material.
Speaking on a visit to a Derry Féile on Wednesday, she welcomed the removal of the pallets.
“I commend those who have removed the pallets and everything else, all the material, because none of us wants to see these anti-social bonfires in our community,” O’Neill said.
Politicians and church leaders had appealed for calm ahead of this weekend.
For a brief period on Saturday night, rival groups taunted one another with sectarian abuse.
A small number of missiles were thrown by both sides.
The police then moved about 30 people away from a section of the city’s walls.
PSNI Area Commander of Derry City & Strabane, Ch Supt Gillian Kearney said material placed on a number of bonfires in Derry “included flags, poppy wreaths, banner/s, political material, sashes, football shirts and other items”.
Kearney added: “The material placed on bonfires in the city is disgraceful, and is to be condemned. It will have no impact on the work we do every single day to make a difference and help the communities we serve.”