Nice question. A few ideas: (1) as you can see from the sources brought in this thread most commentators do not take the phrase to mean literally that the girsa of the mishna needs to be corrected. (2) Even though some commentators do take it that way (e.g., Halichot Olam), we aren't going to mess with the text based on a safek, especially if it's a minority view. (3) Even if the gemara means the mishnah's text is mistaken, the correcting of the mishnah is part of the give and take of the Talmud. Including it is similar to the inclusion of rejected opinions, rejected hava aminas, misunderstood opinions, even other kinds of corrections ("if it was said, it was said like this" or "this is what I meant"). Rashi does sometimes give a heads-up on the Mishnah that the gemara is going to mess with the girsa. Though this third explanation may not explain why we don't make the corrections in printed collections of the Mishnah separate from the Talmud assuming such editions serve an independent, non-talmud-related purpose.