Cutting straight to the chase:
These are just a few of the more obvious plot holes in the film collected and edited from all over.
1) Superman on Earth's air vs Outer Space:
- Superman was so dependent on Earth's atmosphere that when he arrived in Zod's ship, whom according to Zod himself was filled with Kryptonian atmosphere, Superman himself started feeling week, trembling, puking, and then eventually fainted because his body was so dependent on Earth's air. Yet, before and after that scene Superman seemed okay flying into outer space at least twice with not a single sign of any ill effects.
2) Lois Lane surviving a Kryptonian Laser blast that kills Kryptonians:
- Earlier in the film, Superman enters the 18,000 year old Kryptonian vessel. He gets hit with a Kyrptonian laser whiplash that cuts open Superman's arm and he starts bleeding. Lois Lane, on the next scene, also gets hit by the same Kryptonian laser whiplash straight to the abdomen. The force of the blast was so strong, it knocked Lois against a wall, but she survives the blast as Superman saves her and destroys the droid. Later in the film, Lois gets a hold of a Kryptonian gun that shoots out the same beam that kills off super powered-godly Kryptonians with just 1 blast - Kryptonians that can withstand multiple missile attacks mind you, are no match for this laser... yet Lois Lane is. Lois Lane = Wonder Woman.
3) Kryptonians chasing Lois Lane around the Spacecraft:
Continuing above, when Jor-El converts Zod's spacecraft's atmoshpere into Earth's so Superman may regain his superpowers, and so that Lois can escape blasting her Kryptonian captives with above mentioned laser like a highly trained Agent, why were Zod's men chasing Lois around the ship like they had no superpowers. Clearly if Superman got his powers back, shouldn't the other Kryptonians?
4) Black Hole sucks in Zod's Ship and everything else but Lois Lane:
- The Black Hole created by Superman's pod was so strong that it completely engulfed Zod's giant ship, while at the same time sucking in vehicles and other debris including all the Kryptonians trapped in it's vortex... except for one Lois Lane. She manages to fall freely away under the Black Hole waiting to be saved as everything else gets sucked all around her. Lois Lane = Wonder Woman part 2.
5) Zod's purpose of taking Lois Lane prisoner:
- While in detainment, Lois was just locked up and served nothing else in the film. Lois later apologizes to Superman that Zod probed her mind in which she blames herself for the Kent's farmhouse being demolished, to which Superman retorted that it's not her fault and that his mind was probed too, so she shouldn't blame herself. If the writers had left out Superman being probed then Zod's action of taking Lois hostage would have had a purpose in the story, but the the writers didn't. So in other words, that whole scene of Lois' kidnapping was made to serve simply as a plot device by the writer in the story for Lois to meet Jor-El in order to conceive the idea to stop Zod and the World Engine.
6) Superman's Force just by taking off:
- Throughout the film when Superman takes off, the force is so strong that the ground beneath him trembles and even cracks, breaks, and even shoots out dust storms from the force, that in one scene he even warns Lois to stand back in one scene so she won't get hurt. Guess the writer forgot about it because in another scene after Superman rescues Lois, as they were locked in an embrac about to have a moment, Superman in a snap, suddenly takes off basically right next to her with, again, no ill effects. Lois Lane = Wonder Woman part 3.
7) Jor-El's 18,000 year old suit for Kal-El:
- Superman at 33 years old getting his suit made by Jor-El in an 18,000 year old Kryptonian ship that crashed on Earth 180 centuries ago. Lots of stuff left out and left for the viewers, like Clark, to just nod our heads and just go with it.
8) Zod Terraforming the Earth to become Krypton:
- Zod not only wanted to rule the Earth but he also wanted to terra form it because he didn't want to have to "suffer years of pain adapting to its atmosphere." This is the same atmosphere that make him and other Kryptonians basically gods on Earth, and yet he wants to make themselves like earthlings. It's just not a good plan for world domination.
9) Superman breaking Zod's neck as the only option:
- "Why did Superman kill Zod?" That is the WRONG question to be asking. The real question is, did Superman even have to kill Zod in the first place? All it takes is for either: A) The family on the corner to move out of the way by going forward instead of continually inching to the right. B) Remember that Superman had Zod in a headlock in other words he had full control of subduing Zod which is the purpose of a headlock, so simply tilting Zod's head any other direction but right should do. Or Superman can basically just flying Zod in any other direction away from the family; tossing him works too - that's all they were doing to each other just the scene before that. In other words, breaking Zod's neck could have even been avoided.
10) Destruction in Metropolis, Rebuilt in the end:
- The City of Metropolis as a whole was in shambles practically billions of dollars in destruction including the Daily Planet. But the ending shows everything seems all fixed and built up again. Do we assume the ending took place some 3-4 years later for the city to completely finish rebuilding?
11) Army picking up Superman's Pod in the Kent Farmhouse:
- An army transport helicopter arrives holding Kal-El's pod. Question, how did they get it? The last scene before that shows Superman arriving at his home to witness the carnage, almost at the same time Lois Lane arrives with the police escorting her. At this point, the pod was still housed inside the Kent farmhouse... but now with police and army surrounding it. Shouldn't take long for the army to deduct that the guy with glasses named Clark Kent, whose farmhouse the pod was taken from, who by the way also looks like Superman is... which brings us to...
12) "Clark"... Superman's Identity:
- Besides what happened above, Lois basically calls Superman "Clark" twice out in the open when cops are present. The army's satellites knew where the Kryptonians were landing, with cops arriving by the Kent's farmhouse. Not to mention the dozens who had witnessed and know Clark perform superhuman feat. Understand if this was the 50's, but the type of information gathering this decade has now? Explanation hopefully will be in the sequel, until then, good luck with those glasses.
13) Martha Kent too trusting of Lois before doubting:
- Upon first meeting Lois asking about Clark, Martha basically invites her in and gives away her son's secret when she tells Lois about Jonathan's death and his grave. But then later, when Clark stops by, Martha asks him if he thinks Lois could be trusted.
14) Superman saving Jonathan Kent while keeping his secret safe:
- Superman is so fast that he could zip away from a direct missile attack; So fast he could fly across the Indian Ocean on the other side of the world from Metropolis, topple a World Engine, then fly from the Indian Ocean back to Metropolis again before the military could even reach the Daily Planet. Yet we are to believe that Clark can't just quickly get the dog while he was still near the family car. Or even after Clark had taken his mom to safety, rather than run after his dad, he just stands back and watches Jonathan go running back to the car, try to unlatch the door, get trapped inside, let the dog out, witness a vehicle hurl towards Jonathan, see vehicle slam above Jonathan's car, watch him struggle some more, before getting out just to see him get sucked by a tornado.
15) Lois climbing some thousand foot Mountain in the North Pole:
- While the army and archeologists do nothing but send out helicopters to take images of the mysterious 18,000 year old ice/vessel while they sit below the mountain in their nice warm tents just marveling what it could be, Lois decides to brave the ice and actually climb the mountain herself to reach the Kryptonian vessel. Why the army/archelogists didn't hire her alludes me. Lois Lane = Wonder Woman part 4.