The Marvel Cinematic Universe has given us some gems over the years. It's almost perfect. Think about it. They set up Thanos as the big bad in 2012 with a post-credit scene and built his character one such scene at a time. 

But like I said, almost perfect. The MCU has a few plotholes that you can very easily miss between all the brilliant storylines and the mind-boggling CGI.

1. If the Bifrost was so easily built, why did Loki tell Thor that if he broke it, he would never see Jane again?

At the end of Thor, the God of Thunder breaks the Bifrost with Mjolnir to stop Loki from destroying all of Jotunheim. 

Source: The 300s

In The Avengers, we find out that Odin had summoned dark energy to ship Thor to Earth. And then in Thor: The Dark World, the Bifrost is back and fully functional without any explanation.

Source: Stack exchange

If building the Bifrost was so easy, then why did Thor mourn not ever being able to meet Jane Foster? That seemed a bit too much, given that he is not much of a sentimental type. 

2. If removing the arc reactor from his chest was not a problem, why did Tony Stark need to find a new element to power it in Iron Man 2?

At the end of Iron Man 3, Tony Stark decides that he is Iron Man, with or without the suit and removes the arc reactor from his chest. 

Source: Daily Superhero

So why did he have to find a replacement of palladium to power the reactor in his chest in Iron Man 2, when it was actually killing him? It kind of renders the point of finding a new element moot. 

3. Why did Thor take the Tesseract to Asgard and leave Loki's sceptre behind at the end of The Avengers?

So Thor knew pretty well that Earthlings aren't supposed to be trusted with any sort of mystical objects. I mean, they had the Tesseract. But their experiments to make weapons allowed Loki to invade with an entire army.

Source: Stack Exchange

So why in Valhalla would he leave Loki's sceptre on Earth? And correct me if I'm wrong. Earthlings misplaced that too and the Avengers had to retrieve it from Hydra. 

4. How does Bruce Banner remember everything about Thanos, given that the only time they fought, he was the Hulk?

During the events of Thor: Ragnarok, Banner has no idea that he had been the Hulk for almost 2 years and did not remember a single incident that took place. He was also sure that he no longer had much control over the Hulk.

Source: Film Exodus

However after Heimdall sends him to Earth, he seemed to remember every tiny detail of Thanos' plan to procure the Infinity stones and use them to wipe out half of all life. 

5. There is an Infinity Gauntlet with all the stones in Asgard as shown in Thor

Source: Insider

Now, in Thor: Ragnarok, Hela dismisses that plothole by calling it a fake. 

Source: Syfywire

MCU did a good job of filling this hole but a filled hole is still a hole. 

Thanos, too, has one as shown at the end of Guardians of The Galaxy.

Source: Reddit

But in Infinity War, judging by the conversations between Thor and Eitri it is pretty obvious that Thanos had very recently obliterated them. If Thanos had assaulted the dwarves when Odin was still alive, the Allfather would have intervened to save Nidavellir. 

6. Thor's age is a bit of a problematic factor. 

MCU dates the first appearance of Thor to be in 965 AD. This would make him about 1053-1054 years old by the time Infinity War happens. 

Source: Giphy

Besides, in first Thor film, the God of Thunder claims to have visited Earth for the first time. So how could the Vikings have known about him, drawn accurate pictures of him and worshipped him? The Vikings existed long before 965 AD, when Thor was barely a child. 

7. Tony Stark said Thanos has been haunting him for 6 years but Spider-Man: Homecoming contradicts that.

Set in 2016, Homecoming states that its events happened 8 years after the Battle of New York, which places The Avengers in 2008. 

Source: Tenor

But Infinity War takes place in 2018 and Tony Stark tells Dr. Strange that Thanos had been in his head for 6 years, placing The Avengers in 2012.  

9. Tony Stark perfects the Extremis to rebuild the human body in Iron Man 3 but never uses it again.

In Iron Man 3, Tony Stark perfects the Extremis to save Pepper Potts' life. Now Extremis can regenerate entire body parts. But Tony never uses it again.

Source: Reddit

Not even when Rhodey gets hit by Vision and gets paralysed from below the waist! 

But hey, don't take it too seriously. Nobody could have planned an entire cinematic universe perfectly 10 years ago.