There was only one shotgun and it was the one found in the vehicle per police reports.
More than likely they searched his vehicle and the trunk and found that shotgun before going into the school. A mother was interviewed by the media who was there at the front door at that time while there was still shooting in the school and saw the doors of the vehicle open and stuff from inside the vehicle strewn about outside the open doors. Odds are they popped the trunk and found the shotgun then.
That doesn't make any sense. Cops are responding to an active shooter in a school with hundreds of kids. I find it unlikely they will stop and search a car that has a yet unknown link to the crime prior to going into the school to take out the shooter.
The statement prior makes it even more unusual:
9:53:25: “Newtown’s reporting one suspect down. The building has now been cleared.”
9:55:25: “Be advised, we have multiple weapons. One rifle and a shotgun”
Suppose they did find the shotgun prior to entering the school. They they find a dead Lanza who killed himself with a pistol. Why not report "multiple weapons - a rifle, shotgun and two pistols"?
I'm not a conspiracy theorist but from the beginning I've found it strange that everyone says that the .223 would be the weapon of choice for this when clearly it would be the semi-auto 12ga shotgun. The only reason I can see Lanza not using it because it would probably have knocked him on his ass. But then, why bring it?