Scenario: The alien mothership computer was unaffected by the virus
OH, THE MYSTERIOUS ALIEN COMPUTING SYSTEM ISN'T COMPATIBLE WITH YOUR GODDAMN APPLE OS? Christ, Goldblum, smart move. Now you and your cigar-chompin' alien face-puncher are stuck inside THE MOTHERSHIP, they know you're up to no good, and your entire plan to save the world has completely fallen apart. Then again, your plan was "send the aliens some malware and hope they open it." Shit - even if your Mac virus WAS compatible with the alien computers, were you banking on their mothership not having virus protection? Even my grandma's computer has virus protection - we have to imagine a race of aliens trying to blow up every monument on Earth would take AT LEAST those precautions.
Scenario: Tony is caught by his captors trying to build the initial Iron Man suit and his work on the missile becomes more heavily scrutinized
I know that you don't think much of these backwards-ass terrorists, Tony: they have enough connections to successfully ambush a military convoy AND kidnap one of the richest playboys in the world, but they can't just buy some black market missiles? They need YOU to build them one? Regardless, they leave you with a bunch of spare parts and you decide - hey! With these missile parts, why don't I built a metallic suit of robo-armor for myself that will be extremely clunky and difficult to maneuver? That would be fine (actually, there are a bunch of issues with that idea, but whatever), except these terrorists PROBABLY don't place a whole lot of trust in you. They're not just going to let you build helmets and chest-plates and flamethrowers - they're going to be paying attention to what you're working on and keeping you under surveillance the whole time. You're a PRISONER, don't forget. Or were, at least. Now you and your excessively-managed facial hair are dead.
Scenario: The Nazis and Beloq open the Ark of the Covenant and their faces don't melt off.
What are you even doing here, dude? Like, I get you wanted to rescue Marion, but beyond that...what the hell? The bad guys are opening their superweapon and your plan is to shut your eyes and say "LA LA LA LA I CAN'T HEAR YOU LA LA LA LA"? If you were so certain the Ark was just a death machine, why not just let them take it back to Hitler - you know THE DICTATOR GUY WHO WANTED THIS THING? It'd be pretty nice to see HIS face get melted off, right? You're supposed to be the hero - you HAVE to have something more to contribute than shutting your eyelids, right? But nope - that was all you had. Now the Nazis have a superweapon that you had plenty of chances to destroy and are definitely going to win World War II.
Scenario: Crossing the streams does exactly what Egon predicted it would do earlier in the film - every molecule of their bodies explodes at the speed of light
YOU HAD ONE RULE, EGON. ONE FREAKING RULE: DO NOT CROSS THE STREAMS. I don't care how many androgynous Sumerian gods you run up against, or how many enormous marshmallow creatures you're stuck battling - you're the brains of this operation, and you specifically said to never do the thing that you later said "eh, on second thought, let's give it a shot." Now you're all blown up, New York has been wrecked by an angry god and your own nuclear carelessness, and the EPA is gonna be justifiably pissed off. At least now we'll never have to watch Ghostbusters II.
Scenario: The ragtag group of oil drillers were unable to blow up the Texas-sized asteroid heading towards Earth
OIL DRILLERS? BEN AFFLECK?! WHAAAAAAAAAAT?!
You know what? Thank god the government stopped funding you guys.