Police had attended the alert after a suspicious object was discovered at Butcher Gate shortly after 23:30 BST on Friday.
It was later declared a hoax.
During the clearance operation, fireworks and petrol bombs were thrown at police in the Fahan Street area.  There were no injuries reported.
Police said it was also reported that the windscreen of a van was smashed in Fahan Street shortly after midnight.
Twenty-five petrol bombs and a number of fireworks have been thrown at police by youths following a security alert in Londonderry.