I'm leaving out things which appear to be missing or that work in some fashion which is unexpected since we don't know what Tarn Adams means to be happening. These are just things that clearly appear to be intended to work, but don't.
1. Military doesn't equip properly all the time. Some will wear both gauntlets and some won't, and it shifts randomly if you disband the squad and start over. Sometime they will wear caps and helms together, and sometimes not. Same with mail shirts and breastplates. Retrying the dressing sequence several times sometimes fixes the problem but not always.
2. Dwarves don't respect bed assignments, including using up all the bed space in the hospital instead of sleeping in their own rooms. This results in bad thoughts from sleeping without a proper room as well as making it impossible for wounded Dwarves to get treatment. Burrows help somewhat with this, but not with the hospital. Restricting the traffic zones is useless for this purpose. Even a cost of 100/per square won't stop healthy Dwarves from sleeping in hospital beds.
3. Gypsum powder won't store in the hospital and people want to wash in inaccessible water sources if you give them soap.
4. Buckets of stagnant water accumulate in the fortress and the water cannot be dumped from them. They come from people attempting to bring water to thirsty Dwarves who are actually healthy and often already drinking from a barrel when the water arrives. This stagnant water gradually evaporates, and the buckets can be recovered once empty. Lyemakers use buckets containing stagnant water for their operation and you end up with buckets containing stagnant water and lye. These buckets are totally useless. Milkers will use buckets containing stagnant water and thus recover them, but not ones containing lye and water. The water is dumped at the milking station. However, milkers also take the buckets from the hospital.
5. Some of the stockpile settings are borked. Certain things can't be designated but are still stored in the overall catagory, and certain things have designations but they don't work. Raw hides are one example of the latter. Blood is one of the former.