These ones are only tangentially related to the topic at hand, but maybe the right person reads them.
I do remember being very confused over minor simple things when I started with the game, which just went into the background after a while. DF sorta gets into your head like this. Anyway.
Leather. Butchering a creature produces a skin. A skin is tanned into a piece of leather. A piece of leather is required for any one job. Ergo, both a dog and a sperm whale produce the same amount of sewing material. Which was just... mindbogglingly wrong at the time; you'd think a game that simulates entire civilisations can tell a dog from an elephant, but when it comes to leather caps, it clearly can not.
How to fix this? Treat skin like ore: one item is processed into multiple material items, which are then used in varying amounts to make clothing. Cloth should also conform to the new framework. That is the realistic way. The right way. Cloth should be treated the same as metal for interactions, regardless of whether butchering a creature will produce a stack of skins like with bones (realistic approach, try tanning all those whale bits before they all rot) or a single 'pelt' that will tan into a dozen leather items (quick approach).
Blocks. I saw where the game is coming from by making a stone chunk process into multiple blocks - you can't fit a round boulder into a square hole but after you cut... ... scratch that, it makes no sense now and my brain hurts. What do we have? Making rock into blocks quadruples its volume; making wood into blocks doesn't change it; making metal into blocks divides volume by 3 (by 4 if you count the charcoal). One unit of raw material or a block is required for any job, so block size is a constant... Bloody hell.
Okay... The block item is an abstraction. An inconsistent abstraction, which is even more jarring. We can have individual toenails but can't count our bricks... Okay. First, for the love of Armok, make blocks consistent. Then the issue can be approached from two opposite ways: either make blocks into actual bricks (with multiple being needed for just about anything), or forbid building walls from raw materials (and make raw stone/wood walls into 'Barricades', a variation of Vertical Bar), or maybe even both. Rename wooden blocks into 'Plank's. Masterwork did have the right idea with their chopping block workshop - lumber should require some pre-processing, just not as much as metal.
I can probably name a couple more logic holes, but these ones I still remember from way back then. The game will be easier on the noobs if it consistently makes sense. Let's be honest: all that intrigue and other fancy world-gen stuff may feel like epic world-building, but it's essentially just window dressing for what actually happens on screen - dorfs building things. I just can't appreciate the fluff if the crunch is not solid enough. Neither will others.