All the evidence is there, you'd have to be a retard to deny it. If they avoid each other that obviously and that earnestly, something really shitty must have happened between the two.
My guess? I think it has to do with Pekora being asocial and, as said by Miko herself, "rarely inviting" Miko to the stream like she said in this video
>>2076952, while Miko herself is an overzealous personality. Perhaps Miko brought up Pekora's said lack of enthusiasm to collab, which then prompted a malicious response from Pekora. And that's how we got to where we are today.
I believe this to be the most logical conclusion.