Arelith

Invisibility has for the longest time not worked as expected when it comes to NPCs. This applies to every enemy type there is from lowest level to highest with no discernible ways of seeing invisibility.

Problems

NPCs keep chasing you after you've cast invisibility. I assume this is because the last command given was an attack and they need to complete their last flurry before they check to see that their enemy is in fact someone they can see. You have to stop and let the enemy finish their attacks to make them stop chasing.

NPCs aggro you despite lacking ways to see invisibility. After casting invisibility you'd expect to stay undetected, specially at a distance. However, this is not the case. You often have to combine both invisibility and stealth mode in order to stop enemies from aggroing you again.

Solutions

Make it so NPCs periodically check to see if their opponent is invisible and stop attacking if that is the case. This would prevent them from autolocking on the player.

Prevent enemies from outright aggroing you when you're invisible, unless they have the needed buffs or attributes. I'm not entirely sure how this bug - and I do believe it's a bug - occurs but at least as a player it feels as though I haven't cast invisibility at all.

I'm more inclined to think they got close enough to hear you and continue.
If it worked as intended, any NPC with any half-decent Listen score would notice you from across the room. Invisibility does nothing to make you move silent, as you're not even trying to remain so.
A level 2 spell doesn't turn you into a trained ninja (nor should it).
Heck in pnp, invisibility is noticed by a dc 20 spot check just because you do things like stir up dust or step on grass, etc.