To spell it out, Parrot the project started around the same time as Perl 6 the project. Initially, a lot of Parrot's purpose in reality was to be a VM for Perl 6, but Parrot also had a goal of being a good general VM for dynamic languages. From that perspective, I think they were often mentioned together because neither wanted to be overshadowed by the other to the point of obscurity, and they wanted to draw on the general audience each might bring (and there were quite a few people doing stuff in Parrot with nothing to do with Perl 6 eventually).
Did it cause problems? Probably, even if you ignore the eventual blowout they had. That doesn't mean it was it was entirely a stupid technical reason by technical people ignoring marketing concerns, as part of the reason I think it was done was purely for marketing. Initially, it might have even helped (a VM for dynamic languages was a big idea back then, I know I saw a lot of people excited about it).