What does a specialization in weapon skill (parry) or coordination (dodge) do? you never make parry or dodge checks and the parry and dodge cards don't mention any bonus for specialization.

Possible fixes

1. give a third black dice if you have relevant specialization (might be overpowered)

2. only give the second black dice if you have the specialization

3.let them use there dodge specialization to dodge traps as an agility test. (can't think of similar use for parry)

They don't affect the Active Defense cards, as explained in page 6 of the FAQ / Errata:

Specialisation: Active Defences
Several skills indicate specialisations most commonly associated
with the Dodge, Parry, and Block active defences. These specialisations
do not affect the use of the active defence cards.

However, if the GM asks the player to make a skill check based on
dodging, parrying, or blocking something (such as in a case outside
of a direct incoming attack directed against the character) the extra
fortune die would be added to the dice pool.

These specialisations are noted in the skill descriptions because a
particular specialisation may be a pre-requisite for certain action
cards in the future.

That being said, I wouldn't put it past me to give the extra misfortune dice in actual play in certain situations.

They mostly seem to fit with the scenario you describe in your last point.

in my house rules the pc or npc (i mean the opponent attacking him/her) my purchase the "Master Parry/Dodge/Block" Action Card . This card adds an additional Misfortune Dice . Prerequisit is that he/she is specialized in Parry/Dodge/Block and has the " Improved Parry Action ". And if he has trained the skill all 3 times and he has specialized it the Misfortune Dice Turns into a Challenge Dice .

Also if the Parry/Dodge/Block is sucessfull and the Attacker rolls a Chaos Star the Defender gains a free "Melee Attack" Action with an additional Misfortune Dice or a free Maneuver against the Attacker.

This rule is valid at our gaming table until FFG releases similar rules or Actions for this.