Say a PC had two attacks and goes before in initiative with an NPC. The PC manages to hit with the first attack and causes damage, but the second attack misses and on the combat chart allows for a counter. Does the NPC still get the counter even though hit? And does the NPC get to continue attacking even though the NPC was hit by the first attack?

No, because if a character gets hit in anima before their intiative they lose their active action. So the NPC who got hit loses his ability to counter attack, they can use their minor action though.

Is a minor action a passive action?

sorry yeah played so many systems I get them mixed up.

Sorry for the late gratitiude but Thank you, for explaining that to me.

It's all good, glad to be of help. Been playing and GMing Anima for months now and some of it still goes over my head