I think the biggest most obvious issue with bots, mods, and such is that Square-Enix is very tolerant of such behavior. To the point where the community has began to openly accept their usage--despite being against the ToS. Because Square-Enix doesn't dictate a 'zero-tolerance' on such behavior like other gaming companies it leads to a lot of gray areas. And because of that, the community for such has flourished. I would imagine the biggest misunderstandings come from the top. Where people are confused on Square-Enix's stance on such activities.