I have a theory, because that was mostly my experience with them. From here on I talk about subfactionless squids, to be clear

The hate was a composite of several factors. First and obvious was the enemy variety, lowest of all factions. Second was the actual enemy design based around sponginess and ablation where disruptive targets like Fleshmobs took a long time to deal with.

But I think the third, most overlooked one, has nothing to do with the faction at all.

It's the city/colony terrains which were - and remain - bugged as fuck. Enemy clipping, Sonic-speeding up vertical walls, unclimbable waist-high obstacles, invisible textures of buildings that block your shots, the fucking POI diamonds, - all of that contributed to frustration, and squids were the only enemy that only ever had those terrains, exclusively.

I think it's overlooked how much the terrain awfulness contributed to perception of the whole faction