A web is a hostile spell, so when enemies walk into it, it will break invisibility since the enemies are now being hit by it.
If you're "fixing" this, then don't forget to fix all the other AoE spells to have this effect too.
I would love to be able to cast Grease, Web, Entangle, Spike Growth, Darkness, Wall of Fire, Acid Fog, Cloudkill, Stonehold, Creeping Doom, incendiary cloud etc etc on the ground, drink an invisibility potion after and be perfectly safe as I use summonings to lure enemies into the mess.
Conversely some wizards might be a tad annoyed if when casting offensive AoE spells if it broke their invisibility simply for the casting if nothing walked into it. They may have to change their field setup strategies.
The nwnwiki gives these conditions for what breaks invisibility, which has been the usual behaviour for invisibility, so the spell is working as expected.
"Attacking, or performing any hostile act, causes invisibility to be lost, though. This includes hostilities performed by a lingering spell (cast by the subject before becoming invisible), but does not include summoning a creature nor hostile actions taken by a summoned creature."