Wolves will write to UEFA to ask why Espanyol sold tickets to travelling fans in the home end.
The club are unhappy their Europa League rivals openly allowed Wolves supporters to buy the seats, the PA news agency understands.
There was a small scuffle at the start of the second half in a corporate section of the RCDE Stadium on Thursday and some fans were ejected by stewards and police.
It was away from the official travelling section, with Wolves having been allocated 2,100 tickets.
Nuno Espirito Santo's side lost 3-2 in Barcelona but progressed to the last 16 6-3 on aggregate.