Is...is this supposed to happen!?

[Black Boo]

I don't think Jovani actually triggers their appearance, like how you can get the Golden Bugs before you meet Agatha (that was the little girl's name, right?).

Yes, you can indeed find the bugs before meeting Agitha, but why would nintendo sic undefeatable enemies at you before you're ready? That's the real thing that makes me wonder, and I've never actually had this problem before.