People were seen throwing stones and setting a motorbike and a rubbish bin on fire, according to a Reuters witness.
Earlier on Wednesday, hundreds of migrants tried to force their way past tightened security into Ceuta, as Spain pressed on with the expulsion of thousands who had swum or climbed into its North African enclave over the past two days.
The rush of migrants began on Monday (May 17) when Morocco appeared to loosen border controls, a move widely interpreted as retaliation for Spain's hosting of a Western Sahara independence leader.
Around two-thirds of the roughly 8,000 migrants who made it to the Ceuta enclave, including unaccompanied children, have been expelled, Spanish authorities said, though many of those returned said they would again try to reach Europe.
On the northern tip of Morocco across from Gibraltar and with a population of 80,000, the enclave has periodically been a magnet for refugees seeking a quick way into Europe. But Rabat has cracked down on border traffic in recent years.