I noticed I somewhat misphrased the question. Illogical thinking and illogical writing is more what I mean. So, I know some can be attributed to 'anime logic', but the small irritants add up:
1) "You must have ulterior motives if you compliment a man to his face."
I've complimented my friends a hell of a lot. Especially when we're drunk. Not to mention he didn't have any established motives yet.
2) When Senku hides the 4th use for lime, why does Tsukasa jump to the conclusion that they're making a weapon?
In a survival situation, I wouldn't tell my biggest adversary how to knit a sock, why does he immediately assume it's about weaponry?
3) Tsukasa assumes they want to make a weapon to defeat him when they flee
Or... They don't want to be around him, because he explained the inner macinations of his messiah complex before the human dust even got washed off his hands. You'd reckon people would run, because they don't want to get murdered in their sleep
4) Tsukasa assumes they're traveling to Hakone when he see's footsteps to the west
This is the big one that really pissed in my cornflakes. I swiftly browsed through the first couple of chapters in the manga to see if anything got explained, so I could properly write this response, and while I found out some of my irritations were anime only, I've confirmed They haven't even told this motherfucker where he is yet. Let alone with such pinpoint precision that he can guess precisely which city is close enough for a trek. Sure he might know where Hakone is, because he saw it on a map somewhere, and sure he might know there are hot springs brimming with sulphur, weird as that is already, how does he know they're going to make gunpowder to make a weapon in an attempt to kill him? This dude is an MMA fighter, you'd reckon he's never even thought about how to make gunpowder, and yet he knows. Does his schizophrenic paranoia align the stars allowing him to be correct at all times? Nevermind how he thinks a kid with 0 tools he just met a mere days ago could build a gun from scratch in this world. Senkuu is smart, and he definitely could, but how would he ever know this? If I was Tsukasa and Senku was Albert Einstein or Nicola Tesla, I wouldn't even assume this.
5) If Senkuu needed a sextant to navigate to Hakone, how did Tsukasa get there?
Sure you can track someone, but besides an IQ of 145, MMA prowess and enough knowledge of basic science that you could've probably just killed Senkuu on sight and figured out how to make the reviving potion yourself, you'd be taking a massive amount of piss if you were to also tell me this highschooler was an expert hunter. I know it's anime logic, but it has to be somewhat logical even in the anime.
6) Why does Tsukasa assume Senkuu won't break his pinky promise if it's about science?
Genuinely what?
7) Why didn't Senkuu just say no?
I can understand empathy getting in the way of logical decisionmaking, but for a man that's all about logic, he could've just said 'no'. The new age of mankind having a sociopathic, murderous ruler hinges on it, and he's just cool with potentially getting killed.
8) Tsukasa knows exactly where to hit to grant a painless death
So this dude's a med student now too?
9) Uzuriha figuring out Taiju's plan immediately and immediately reacting
Your only hope of mankind's proper revival just got killed in front of your eyes and your thought process is so crystal clear that you can figure this out in a split-second?
10) Tsukasa should be able to see his hostage running from his peripheral vision even if he's focused
11) Tsukasa assumes Taiju probably didn't want to hurt him by throwing the rock
mate he threw a rock, I don't think he knows precisely where it's going to land, or even where it needs to land.
I reckon there's some more I missed while glossing over, but all these things really added up.