Yeah, I know, her braid should be on the left side. It's even a plot point in the manga. That said, Marisa's hair style changes from time to time, much like her clothing, so it's hard to get too upset over somebody getting it wrong.
I was also going to bring up what >>14826056 said, but I thought about it for a bit this morning and it occurred to me that the only two games that have Marisa's braid on her right side (IN and the first three fighting games) had the excuse of utilizing sprite flipping. ZUN probably designed, or in the case of the fighting games, had someone else design, her has an enemy sprite rather than a player sprite, and simply flipped her enemy sprite for her character portrait.
And that got me thinking, it would actually be really easy to fix the braids positioning in most cases, so I suppose that I should start doing that.