The following feats are bugged or non-functional in NwN2 in general.

Alertness - If the character has a familiar, unsummoning it will make you lose Alertness feat permanently. This is especially annoying for characters that want to enter into Harper agent prestige class.

Blind Fight - The +2 bonus to hit that invisible creature should have against a sighted opponent was never implemented in NWN2, so there is no damage bonus which the feat negates. The in game description was copied from the PnP source.

Darkvision:  This can only be granted by race or class features.  Spells or items that supposedly grant darkvision will have no effect.

Death Attack - does not count as a Sneak Attack for the purpose of qualifying for feats or an additional PrC, even though it should.

Deathless Mastery (Pale Master lvl 10) - "Currently, Deathless Mastery is not providing immunity to sneak attacks. 

Defensive Stance (Dwarven Defender lvl 1) - Any spell or spell-like ability or even Whirlwind attack cancels the effect of this combat mode but doesn't deactivate it.

Disarm - While not technically bugged, creatures in the toolset are unable to be disarmed by default. As such, most creatures end up unable to be disarmed, making this feat and its improved variant mostly useless.

Evasion - As of v. 1.12, characters in medium and heavy armor benefit from Evasion.

Extra Slot - When determining the highest level of spells a character can cast, the game only takes into consideration levels in a base caster class, e.g. levels as cleric or wizard. Levels from a prestige class such as Red Wizard or Arcane Scholar of Candlekeep are ignored. This means that a level 5/10/10 Wiz/RW/ASoC, for example, can only take Extra Slot feats for spell levels 0 (cantrips), 1, and 2, respectively, although that character can cast 9th level spells. 

Extra Turning (And all Divine Feats) - In base game, these have a bug where you can only select then if you're taking the feat-gaining level in the class that can take the feat. However, ALFA has fixed and has implemented the fix so that you can take the feat any time, with any class level, so long as you meet the prerequisite.

Flurry of Blows - Flurry of Blows and Greater Flurry of Blows both give one more extra attack than they should at the end of the main-hand attack schedule. This attack does not apply the normal penalties for using Flurry of Blows or for dual-wielding, if the character happens to be using two weapons. This extra attack is applied even if the character is using flurry while wearing armor or using a shield.

Improved Disarm - As of version 1.12, this feat does not work as described. If you disarm your foe while carrying a weapon, your foe's weapon will fall to the ground. If you instead disarm your foe while fighting barehanded, your foe's weapon ends up in your inventory. In addition, see Disarm above.

Improved Uncanny Dodge - Nonfunctional

Light Blindness - This is improperly applied whenever a light blind character is outdoors, even during night time. The attack and saving throw penalty are only applied on the character sheet. They are not applied to the rolls in game. Characters are also affected in certain indoor areas.

Light Sensitivity - This is improperly applied whenever a light blind character is outdoors, even during night time. Characters are also affected in certain indoor areas.

Pilfer Magic - Note that the spell description is wrong. First, no touch attack is involved here. Second, this spell is definitely not equivalent to Lesser Dispel Magic, but to targeted Mordekainen's Disjunction (no level cap), meaning a level 30 caster (max level you can reach in NWN2 with expansions) can reach a caster roll of 50 (1d20+30)! Fortunately, this is not likely to happen, as the spell uses the caster level of the caster's base class that gave him access to the Arcane Trickster prestige class (so a Sorcerer 3/Arcane Trickster 4 casting Pilfer Magic rolls 1d20+3). However, bugged abilities like Practiced Spellcaster may increase the caster level at which this ability is cast. 

Practiced Spellcaster - Contrary to the description, the extent of this feat is not capped by the character's hit dice, but by the number of levels in additional classes. Normally, the use of this feat operates as described above. However, if used in conjunction with a prestige class that grants additional spellcaster levels, this feat STILL grants up to +4 caster levels and does not cap at the character's HD as it should. Thus, a Wizard 10 / Eldritch Knight 10 that is using this feat will, in fact, have a caster level equal to 23 (Wizard 10 + Eldritch Knight levels 2 through 10 + this feat 4). A Wizard 10 / Eldritch Knight 2 would have a a caster level of 13 (10 from Wizard, 1 from Eldritch Knight, and 2 from the feat).

Precise Strike - Contrary to the description, this ability does work against opponents who are immune to critical hits. The bonus damage is not multiplied on a critical hit. It will not work if you have a shield or a second weapon equipped, but it does work with two handed piercing weapons (e.g. you can make a spear duelist). 

Quicken Spell - Note: Apparently NWN2's handling of the feat allows for quickened spells to be vulnerable to disruption if damaged while casting, likely due to the fact that it's not truly a free action but takes 3 seconds (see below) to cast a quickened spell in the game.

Stunning Fist - As of patch 1.23, Stunning Fist does not work on creatures immune to mind-affecting effects

Trackless Step - The in-game feat description inaccurately states that Rangers gain this feat at level 1.

Uncanny Dodge - Nonfunctional as of 1.23.

Undead Graft - Works, but does not alter character appearance.

Whirlwind Attack - If there are no enemies within close enough range at the time that this feat is activated, the game will appear to "hang" and not make any attack attempts at all. Cancelling this action and attacking directly is the only way to break out of this state. This will also have the effect of moving the character close enough to the enemy to actually make use of this feat once again. It is possible to be close enough for the enemy to attack but not quite close enough for this feat to properly active. To ensure proper activation, it is recommended to close to attack range and actually make at least one attack PRIOR to activating this feat. Repeated activations of this feat (1 per round) are possible but can result in the "no attacks made" situation. Careful observation of the character in question is required on the use of this feat.