Explain the following plotholes...

These questions will be answered in the 4 and a half hour Super Extended Ultimate Edition of the film.

This is a far-from-perfect obviously flawed movie in so many ways, but I still like it. And I think most of these can be credibly answered, although there are many other weaknesses that can't

* Lois needed to use her highest level contacts to track the ammo, so it took her time, which is all Lex needed. He never wanted to "get away with it." He was OK getting jailed or killed, as long as he succeeded in making Superman look like a monster. That's why he's more like the Joker than Luthor

* they didn't accuse him of shooting people; they flamed everyone and claimed Superman did it with heat vision

* Lex knew all along exactly who Bruce and Clark really were, and what Bruce was after. His security measures were only strong enough to be credible - make no mistake, he wanted Batman to steal the kryptonite. Doomsday-Zod was just his backup plan

* Batman "fought his way up" presumably because the "hostiles on the third floor" were expecting him to come in from the window or the roof (since they knew he had a flying machine). Aside from the obvious dramatic effect and homage to Miller's Dark Knight comic, attacking from below gave him the advantage of surprise

Admittedly, when the fight scene went on as long as it did, that negated the surprise element. If he could've beat them all that slowly, then he didn't need to surprise them

* It's not so easy to track, and even when it was, Lois can't even prove it, the only confirmation she had was unnoficial by A GENERAL who still was afraid of losing everything for telling it to Lois. Plus, Lex himself says those evidences will vanish like sand in the desert.

* Nobody suspected that, the corpses were incinerated to look burned by the heat vision, and a biased forensic analysis would point the accusations to Superman

* Ahem, Lex is the one who wants Bruce to take the kryptonite from him, he even says so: "I gave the bat the weapon to destroy you". He just acts like a fool, while manipulating both Clark and Bruce. Even in their faces (when he introduces one to the other, he already knows who's who, and makes jokes about Clark's strength) but everybody underestimates a guy who acts like a fool. It's one of his tools.

* Superman didn't save Martha, he was needed in the ship against the creature. Batman decided to fight from down to upper for technical reasons a 20 years career crimefighter would understand (I mean, Alfred sugests the second floor as if it was something they've tried before!)

*Why would you equip your secret commandos with ammunition that can be traced back to you by some reporter?

. . .You wouldn't.

*And why would anyone suspect Superman of shooting people? He has never used guns and can kill far better without them.

. . .They wouldn't.

*And why would you not lock the door to your secret files and not even bother to escort the wandering billionaires away during your parties?

. . .You wouldn't. . .

*And why didn’t Superman go save Martha when he could have done so by crashing through the ceiling, instead of fighting his way up.

Hm. Did you mean Batman? If so, this is the one that a previous reply got right: they clearly sacrificed plot for kewl/fan service, here. It's a nod to the comics.

I'm responding to you instead of the other replies because, as valiant as their efforts are, they basically amount to fanfic that tries to backfill your very legitimate plotholes.

Perhaps the snyder snyder cut will tell all

None of these are plot holes.

Ammo: people make mistakes all the time. expecting someone to trace your top secret bullets isn't exactly a high risk.

Superman shooting: who said he shot anyone? the site was destroyed. he's good at destruction.

Secret files: they were encrypted. no one expects a billionaire to be a super sleuth/spy/ninja.

Martha: Superman knew Batman could handle it, and he had problems in Metropolis Batman couldn't handle. Duh.