What is the only instance in which a team could have a 6-on-3 advantage in OT?

Pulled goalie with two men in the box

Actually even in the regular season IF two men are in the box it is switched to 5-3. They aren't going to let you pile up penalties with the other team only getting a 4-3. So the second penalty you get an extra skater. So you pull the goalie for the sixth skater. It could be regular season or playoffs, where you get a 5-5 normal OT.

Team A takes a penalty which makes it 4 on 3. Team A takes a second penalty. It is not possible to skate 4 on 2, so instead Team B places a 5th skater on the ice. Team B then pulls their goaltender to get the sixth skater.

Either that or there is a bug in the code.

It would have to be in the playoffs, with the goalie pulled for the power play team and two men in the box for the shorthanded team.

It couldn't happen in regular season OT, since that's 4-on-4 play, and the most skaters a team could have on the ice is 5 with the goalie pulled.

You must have your settings different than what NHL rules are for OT. In the NHL, OT is 4 on 4 hockey, at least for regular season, but not so for playoffs, so I guess it would have to be a playoff game, and 2 players in the box with your goalie pulled, probably for another delayed penalty, as once the other team touches, the whistle is blown, so they can't actually shoot the puck in your net. In that case, unless one penalty ends during the delayed call, it would be a stacked penalty, as a team must have a minimum of 3 skaters on the ice at all times.

One team would need to have a two man advantage and then pull their goalie for a 6th attacker.

a 6 on 3 can not happen no matter what in over time. Both teams have 4 skaters and one goalie to start ot so that means there are 5 players max that can be on the ice at any one time during overtime. So this situation is imposable to happen. Even if they have a penalty and the other team pulls their goalie it still can not happen. And there can be no less then 2 skaters and 1 goalie on the rink at anyone time if they have been assessed a 3 man penalty.