Taylor became centre of attention after Sevilla overcame Jose Mourinho's side following a tense penalty shootout.
Mourinho directed a foul-mouthed tirade at the English referee in the aftermath of Wednesday's final, which appeared to set the tone for what was to come.
Taylor and his family were subjected to further abuse at Budapest airport and had to be ushered through a door by police into a more secure area, as bottles and a chair were thrown in their direction.
Refereeing body PGMOL, condemned the incidents stating they were 'appalled at the unjustified and abhorrent abuse'.
However, Pinto appears to have reignited the row and added further criticism after revealing the club had since analysed Taylor's performance.
Read more on Roma
Premier League clubs on red alert with Roma 'ready to sell' Tammy Abraham
Mourinho gives Europa League runners-up medal to fan as Sevilla end his perfect record
"We at AS Roma don't want to raise doubts about Sevilla's merits," said Pinto. "We believe that with our opponents we put on a great final and honoured the stage offered to us by UEFA in the best way.
"We don't usually comment about these types of situations but we've analysed both the most glaring incidents and those seemingly less evident and it is clear that in disciplinary terms the refereeing of the match was not balanced."
Pinto's comments are unlikely to help Roma's cause after the Serie A side came in for criticism of their own following some questionable behaviour during the showpiece final.
Roma took a first-half lead through Paulo Dybala but were pegged back when Gianluca Mancini put through his own net.
Most read in Football
Man United take important step towards signing Mount from Chelsea
French Ligue 2 player taken to hospital as shocking fan attack sees match suspended
Man United FA Cup final blow, Guardiola reveals surprise decision, Mourinho charged
Man United forced into kit change ahead of FA Cup final against Man City
After a tense period of extra time, Sevilla kept their nerve to win 4-1 on penalties to claim their seventh Europa League title since 2006, and a place in next season's Champions League.