Lilgert's lawyer Glen Orris told the court that the instructions from the judge to the jury gave the Crown an unfair advantage, leading to the conviction of criminal negligence causing death.
Orris told the court this morning that the oral charge from the judge to the members of the jury differed from the written charge.
The 125 metre-long car and passenger ferry went down after striking Gil Island, off B.C.'s Central Coast. Evidence at the trial showed Lilgert failed to make a critical turn in the middle of the night.
Two passengers were never found and are presumed to have died when the vessel went down after striking a rocky island in the middle of the night.
Lilgert was convicted of two counts of criminal negligence for causing the deaths of Gerald Foisy and Shirley Rosette.
He was sentenced to four years in prison after a lengthy jury trial that ended last year, but he has been out on bail pending the appeal.
During the course of the trial, the court heard Lilgert was likely distracted by the presence of his former lover, quartermaster Karen Briker, who was the only other person on the bridge with him in the minutes before the ship hit the rocks.
Lilgert testified in his own defence, telling the jury he was busy navigating the ship and ordering course changes and was challenged by rough weather and unreliable equipment.
But the judge ruled that it was clear Lilgert's relationship with Briker was a factor in the sinking.
In delivering the sentence, B.C. Supreme Court Justice Sunni Stromberg-Stein said the "egregious" nature of the crime called for a strong sentence, as it was not an accident or lapse in judgment.