There's actually another way to lose which you didn't cover. If you drive around in your personal car enough, you will get pulled over by a police car and summoned back to the office for a lecture from Captain Hall. After 2-3 times of this happening, he will fire you and you will get a game over with a message similar to "even the hottest detectives need to follow orders." Thanks for your great videos. :)
The two missing deaths mentioned in the comments: "The Captain isn't very happy as he says...'Well, here you are again Sonny! You seem to have difficulty following orders.'" "'Another two days off with no pay!' he rants...'You keep this up and you're gonna wind up owing the department your whole pay check!!'" "Even the hottest detective needs to follow orders." "You and Keith leave the plane, and search around Steelton. You talk to the Steelton police and they are unable to help you." "You and Keith find that Colby has been murdered, but there are no clues." "Two days later, the Steelton police find Marie's body in a gutter, with multiple gun shot wounds to the head." "It really would have been a good idea to call the Steelton police before you arrived - just like the Captain suggested." Looking through SCI, I found nothing about a bad ending.
As I recall, you can get the whole plane section correct and then suffer a game over on arriving if you didn't phone ahead of your flight and set the local police to investigate - in which case they have no leads, investigation stalls, and Marie is found shot dead a few days later.
So many nights after school spent getting that 300th point! Yet even after blasting Bains illegally, I still won the game. Does anybody have an upload of the way to lose by being charged with murdering Bains after firing without warning? Then again, who'd snitch on Sonny? Marie who just saw her meal ticket return to save her?
According to the TV tropes article, ("Earn your bad ending" in the PQ2 folder) Bonds gets fired and arrested for murder. I've never been able to do it myself either though. tvtropes.org/pmwiki/pmwiki.php/VideoGame/PoliceQuest