A new skill type was introduced in January 2015 with the Water card Dietlinde, Soul Salvager. Counter Skill is a % that doesn't affect your deck cards or even the opponents deck cards but it is speciffic to the activated skill of a single enemy card. it doesn't affect all the activated skills but only one of them. That means that if 2 skills of the enemy player activated and the counter skill activates as well it will choose one of the enemy and apply a negate effect as stated by the card.
Counter Skills will not affect Event Skills. It will only affect a portion of an enemy card's skill. Counter Skills will negate both effects of a Double Skill. And it will not reduce the negation effect of an enemy's Counter Skill.
From LOC Support 19/02/2015:
"Counter Skills only affect a portion of an enemy Card's Skill, not the entire Skill. For the example in which you have sent us, the Counter Skill will cut 15% of the Great boost to Fire ATK (15%), resulting in a 12.75% Great boost to Fire ATK."
Example sent was a counter skill of 15% triggering against an opponents great boost to attack of 15%
"Counter Skills activate randomly in the case that there is more than one Card in which a Counter Skill Card can activate upon."
So, if your opponent has three skills that activate and you have a counter skill that activates it will choose a skill at random to reduce the effectiveness of.