What things have you noticed in-game that made you go "WTF?"

The real question here was What things you notice in game that didnt made you go wtf?

Well yeah...

There is an entire chunk missing, I don't know why people keep saying it was a crack.  It doesn't even make sense to even put this scene in knowing what you're going to do later.

I had one scene where Cora and Peebee were superimposed over each other. Cora was dominant, but one side of her face, part of her chest and one arm were blue. She looked like she was changing into a Borg or something.

when the peepee asari jumped on my Ryder. Why did it take 15-20 seconds for an interrupt to throw the clown off my Ryder?

Looks like a crack to me. Figure it's supposed to signal that the air on the planet is really toxic. Only a tiny sliver would have seeped through the crack and it still made it hard to breathe. So when the huge chunk goes missing later, it's pretty much fatal.

Pause menu also pauses AVP cryo pod countdown for research points. Seriously WTF, MW data is much harder to come by compared to Helius and Remnant. I just want to make some cool N7 armor, damnit!

"The planet known as Habitat 7 was one of the "golden worlds" selected by the Andromeda Initiative for early settlement. Signs pointed to a lush and biologically diverse tropical region that could easily support an outpost(...) Habitat 7 is a storm-wracked world with an unbreathable argon-nitrogen atmosphere. Intense magnetic activity in unknown metallic elements interacts with the storms, causing interesting but highly destructive electrical phenomena." /masseffect.wikia.com/wiki/Habitat_7/

Alec could have just switched the helmets with Sarah/Scott every few seconds. The death seems a bit pointless and overdramatic. I got no clue why the whole cinematic showed us the brain cell degradation? It's not like she was 5 minutes without oxygen, the world just had it less, maybe even lacking due to weather phenomenon, but it's still strange. No other hazards were stated on Habitat-7, except some shitstorm that only hurt when hit. No logic to me. Too much simplification for a cheap plot development.

Please correct me, if I'm wrong.

I was expecting the Fusion Mods for the armor to go from 'Fusion Mods of Rapid Development I' to go to 'Fusion Mods of Rapid Development II' in a New Game+ with better stats, an long with the other Fusion Mods, but it didn't do that. Anyone else know if it was supposed to do that?

I have had the same thought, but there are two possible explanations for Alec Ryder's death. The simple one is, there was something toxic in the atmosphere that didn't show up in the scans.
Or, my personal favourite,
(spoiler due to late game content, no idea what the spoiler policy is now, so better safe than sorry)

Are you talking about the big shape over her eyebrow or the left side in general?
The skin is also affected by the orange glow under the helmet,so that must be taken into account. 
I still think it's a crack, because of the oxygen slipping out of her helmet. If there was a big gap there, there wouldn't be a steam gushing out at that point. Like if you put a bag of air in water, if there is just a puncture, all the bubbles shoot out from there, but if there was a big gap, then the air would just exit that way. Like when the helmet is smashed the second time, there is no constant stream of smoke, since the air just exits all at once. 

Thats a nexus escape pod!

Everything from the red line over is gone.  Where the arrow is pointing is not a crack, that's how thick the glass was.  There's a reason no cracks spidered to the left side, because the left side in gone.  If you watch the scene, Ryder repairs his/her helmet from left to right, because the left side was the side that was open.  But it's not really worth arguing over, I guess we'll just have to agree to disagree.