A senior crew member on the Queen of the North testified that staff didn't have a clear interpretation of the regulations over how many people were required to man the bridge.
Under cross-examination, Richard St. Pierre was shown a BC Ferries document from two years prior to the crash that indicates three people were required to be on the ferry's bridge.
"It went back and forth a few times. I think at the time we were manning in accordance with regulations," St. Pierre said of his confidence the interpretation was correct even though the number didn't match the document. "It wasn't black and white."
Two people were tasked with manoeuvring the BC Ferry when the collision occurred just after midnight in March 2006.
The navigation officer on the bridge that night, Karl Lilgert, is accused of criminal negligence causing the deaths of two passengers on the ferry.
St. Pierre told the jury some officers were aware federal regulations stated three people should be involved under certain conditions, but said there were disagreements over those rules.
The court heard that a 2004 memo, written on BC Ferries letterhead, included a table citing the Canada Shipping Act.
It stated the minimal requirements during a navigational watch as being "an officer of the watch" and an "additional person," as well as "a second additional person" during certain conditions.
"Those conditions being restricted visibility, congested traffic density, hazardous navigational situations, the local prohibition of the use of auto pilot and at night," a Crown lawyer read to the witness.
St. Pierre said that nonetheless, he routinely staffed the bridge with only two people navigating and steering the ship at night, although he always had the discretion to direct a third person to join that job.
"You could, (but) you wouldn't get any work done," St. Pierre said, explaining the third person was better used elsewhere.
On the night of the sinking, Lilgert and quartermaster Karen Bricker, whose role it was to actually steer the ship, were on the bridge when it crashed.
The Crown is arguing Lilgert was responsible when the ferry failed to make a critical turn and slammed into Gil Island during its voyage from Prince Rupert, B.C. to Port Hardy on Vancouver Island.
Court heard that BC Ferries has clarified its rules in the years following the sinking. The policy now requires at least three people on the bridge: a senior officer, junior officer and quartermaster or lookout.
The defence is attempting to make a case that inadequate policies and poor equipment led to the fatal crash.
While 99 people survived, the bodies of Gerald Foisy and Shirley Rosette were never recovered.
Also on Thursday, court heard conflicting recollections of how many people were counted in the lifeboats and life rafts as the ferry sank.
Jason LaPorte was a deck hand on the Queen of the North who had been steering the ship as quartermaster just before Bricker took over.
He testified he tried writing numbers on his arm with a pen to try to keep track, but the number keep fluctuating between 101 and 99. He recalled the final head count settling at 99 people.
However, another crew member who testified at the end of the day recalled the group arriving at a final number of 101, following five or six attempts.
"It was futile to keep an accurate count of how many people got into each boat," said Derek Sweet, recalling the flotilla of rescue vessels bobbing in the midst of wind, rain and commotion.
Court has previously heard that it took more than six and a half hours after the crisis began for rescue officials to confirm two people were missing.
Shortly after the ship capsized, some boats carrying women, children and injured departed for the tiny nearby First Nations village of Hartley Bay. Most of the crew and other passengers were taken about the arriving Sir Wilfrid Laurier ship to recover.
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