The third issue is that I've seen it lead to people not considering the character of the fictional characters in full. To take one example, guy I know was planning to work with Cartman as a trickster deity. Now, thing with Eric Cartman is that he's not some loveable Bart Simpson character. A kid angered him. So he murdered his family and then fed them to the kid. Now, if you're 100% sure that you're working solely within your own head, with archetypes, that doesn't matter. However, if you have even a 0.01% doubt that there's a possibility you could be working with external forces, that strikes me as bloody stupid to risk.
I will say, though, I think that's generally a risk you run if you're working with actual trickster deities, too. (I'm actually wondering if Cartman might be closer to the sense of a trickster than Bart; they're not exactly known for being cute and lovable either.) I don't think, therefore, that this is a danger specific to dealing with fictional characters. I would also not necessarily assume (based on the information given; you may know better yourself, I don't know) that the guy talking about working with Cartman-as-trickster wasn't considering the whole entity. People do work with tricksters, danger and all; not everyone necessarily considers "this entity did some really nasty stuff" as a reason to shy away from working with said entity. I don't think that's so much stupidity (necessarily, although it can be), just a different idea of what sort of risk they're willing to take to achieve their goal.