PSNI officers came under attack from youths throwing missiles close to the bomb scene.
Trouble flared briefly on Monday afternoon as a gang of youths gathered close to the Foyle Road cordon and pelted police vehicles with missiles.
In one incident a breeze block was lobbed and cracked the window of a PSNI 4x4 as it was being driven into the area.
Police confirmed on Monday night that a 13-year-old boy was arrested at the scene on suspicion of disorderly behaviour.
He has since been released pending a report to the Youth Diversion Officer.
The trouble in the area came as army bomb disposal officers spent Monday afternoon dealing with the devices before forensic teams in boilersuits moved in.
Earlier – and just hours into the security operation on Sunday night – a petrol bomb was thrown at the PSNI from the Bishop Street cordon.
There were no arrests.
Speaker of the Assembly and Foyle DUP MLA William Hay said such attacks "adds insult to injury" considering that they were the intended target of the bombers.