Fans in the away stand lit several flares during the match, with some being thrown in the direction of the pitch as well as into sections of the stadium containing home supporters.
After the draw, in which Aitor Paredes' late equaliser cancelled out Artem Dovbyk's opener, Bilbao captain Oscar de Marcos and forward Inaki Williams could be seen remonstrating with their fans.
"Athletic Club wishes to express its strongest condemnation of the unacceptable acts carried out by a minority of people who travelled to the Europa League match against AS Roma and who were located in the away stand," Bilbao said in a statement.
"During the match, this small group lit flares and threw some of them into the home stand, contravening safety regulations and tarnishing the image of our fans ...
"Captain Oscar de Marcos, along with Inaki Williams, have let this minority of fans know at the conclusion of the match that their attitude 'is unacceptable'."
Bilbao added that they were working with the authorities to identify the fans involved.
