We are collecting these problems so that there are less bad surprises for us while playing and so that we can plan our builds accordingly. Thanks go out to everybody who sent in their contribution!

If you know about a problem that isn't on the list yet please write a post and name one of the headlines/ categories further down where you think your problem might fit in. Then describe the problem precisely. Start the description with the name of the thing that is bugged. This way I can just copy it into the list. :)

I know there are many things that should work differently by Pathfinder rules. But this list should focus on major issues that don't work as stated inside the video game. Otherwise this is getting too big for me to manage.

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LIST OF MECHANICS THAT DON'T WORK CORRECTLY YET
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Feats
Allied Spellcaster does nothing
Seize the Moment and Outflank state to provoke attacks of opportunity from allies with this feat when you crit, but this does not trigger on every crit but only if the crit is a natural 20. This may be intentional hence Seize the Moment would be a bit strong with wider crit ranges on multiple characters.
Spell Penetration doesn't work for Sorcerers at least
Spell Specialization doesn't work for certain spells, like Dragon's Breath and any spell you can only get from a bloodline or domain. It does work on most normal spells though.
Spell Specialization can only be selected for one spell per character
Vital Strike does nothing
Some state that the team feats don't work at all (those feats that grant bonuses when 2 characters with the same feat are close enough to each other). I know that at least some did work - at least they did some days ago. Let me know if you have more detailed information on this.

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Class features
Mad dog Barbarian: Pack tactic does not benefit pet, neither does (improved) trip work for pets
Paladins can't take channel energy feats, despite having the channel energy prerequisite met.
Ranger, Evasion: For some spells (eg Flame strike) that deal two different types of damage that is halfed on reflex safe, evasion and improved evasion only protect from the first damage instance.
Rogue, Finesse training has no x1.5 DEX bonus for two handed weapons or when dual wielding
Sensei Monk: Lvl 6 sensei advice isn’t able to target allies with ki powers (barkskin and true strike at least)
Thug Rogue: Cornugon Smash Feat + Thug's class exclusive ability to cause fear: If demoralize is activated automatically by Cornugon Smash, it will never cause fear.
Two-Handed Fighter, Overhead Chop (lvl 3) does not work when you only have one attack at low levels or when moving and attacking.
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Domains
Animal domain does not give lore(nature) as a class skill and if taken by a druid doesn't properly level the animal companion.
Community Domain: Guided hearth doesn't grant bonus to save/attack at all
Ecclesitheurges domain mastery: Instead of making a choice between the secondary domains, you have access to all spells granted by the deity's domains at each level, all the time. However, only the spell granted by the primary domain (the first one selected) can be slotted to any spell slot.
Fire Domain: Cleric does not obtain his domain spells
Luck Domain: Divine fortune has no usage limit, can be cast unlimited times.
Madness Domain: Vision of Madness not working
Protection Domain: No boni to saves
War Domain: missing lvl 8 ability
Weather Domain: Druid cannot cast Lightning Lord because it requires cleric levels. To reproduce just level up a druid to 9. Lightning lord will show zero casts even though it should have 2. Take 1 level of Cleric and then it will get 1 cast.
Tristian is missing a 2nd domain
Touch buffs from various cleric domains (glory for example) dont work.
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Bloodlines
Arcane Bloodline Sorcerer: Bonded Item does not work
Infernal Bloodline Arcana doesn't actually do anything as the charm subschool doesn't exist in this game.
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Multiclassing
Cleric + Inquisitor: Levels don't stack for the sake of domain powers
Different spellcasters (Mystic Theurges): If you combine a spontaneous and prepared caster, the class feature that lets you cast spells from one class as one rank higher from the other class doesn't work - you can't use your spontaneous casts to cast prepared cleric spells. Someone else sais this works fine for him though.
Multiclassing with Bloodline classes: If using multiple classes with bloodlines, you can choose a different one for each and if you choose the same one, the levels do not stack. (exception: Dragon Disciple works)
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Items
Acerbic Ring - Does not provide an additional 1d6 to the Alchemists Bomb as the description says
Necklace of Double Cross does not provide the 2d6 damage on melee attacks, nor does it provoke attacks of opportunity on your allied party members.
Bracers of archery Competence boni are not working, or at least don't show up on the char sheet.
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Other problems
All animal companions have a feat that should give them enhancement bonus to attacks and damage per 3 hit dice. Despite the small number next to it growing, they only ever get +1, it only shows in the combat log and stacks with different enhancement bonuses like magic fang
Cleric spell "Magic Vestment" doesn't seem to work. A buff is applied to character but it does nothing.
Touch attack spells may provoke AoO even when the casting was done out of AoO-reach.
Skill: Use Magic Device should allow emulating an alignment for purpose of equiping items. I've made custom character - CN and even with +34 UMD it still couldn't use Blessed Path. (It had heavy armour proficiency)
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UI bugs/ Things not correctly described or indicated
Greater bane is missing in Inquisitors class progress UI
Keen weapons and crit range improovements do work. But this is not shown in the Attack info on the left side of your inventory.
Stinking Cloud affects everybody. Not (only) enemies as stated in the description.
Tactician Leader doesn't get bonus to persuade and perception, at least not shown in UI
Targets in Spell descriptions: Spell descriptions sometimes state that the spell affects "enemies", but often ALL creatures in the area of the spell are affected. Stinking Cloud is one example.
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Pile of shame (Stuff that wrongfully landed up on the list)
Intimidating Prowess seems to work as intended, only giving the bonus to Intimidate and not to Diplomacy or Bluff.