The gemara cites a machlokes between R. Yochanan and Reish Lakish whether the prohibition to break the bones of the korban pesach only apply to an area of the bone which has a kezayis of eatable meat, or so long as the bone has on it a kezayis of meat there is an issur to break the bone at any point. The gemara says that even according to Reish Lakish who holds that the issur only applies to a spot of the bone that has a kezayis of meat, it doesn't matter whether the eatable part is on the outside of the bone in the form of meat, or on the inside in the form of marrow. Either way, there is a prohibition to break the bones. The gemara clearly maintains that there is an issur to break the bones when there is marrow inside (even if there is no meat on the outside).
The gemara cites a braisa to support this point. The Braisa points out that there is a contradiction between two pesukim that must be reconciled. On one hand the Torah says ואכלו את הבשר בלילה הזה implying that all the eatable parts of the korban pesach must be eaten, including the marrow. On the other hand the pasuk says ועצם לא תשברו בו implying that one may not break the bones, even to get to the marrow. We are forced to limit one of these two pesukim. Either we must limit the mitzvah of eating the korban pesach to the meat on the outside and not the marrow within, in order to uphold the blanket prohibition to break the bones. Or we must limit the issur to break the bones to include only marrow-less bones, but bones in which there is marrow one would be entitled to break so that they can get to the marrow. The braisa continues that the latter approach is plausible since we find that there is a concept of עשה דוחה לא תעשה, as if the mitzvah of eating korban pesach would push off the prohibition to break the bones. However, the braisa concludes that since we have an extra pasuk by pesach sheini warning against the breaking of the bones, the Torah is indicating that the bones cannot be broken under any circumstances, even to get to the marrow inside.
Tosafos asks, why would we need a special pasuk to teach not to break the bones. The concept of עשה דוחה לא תעשה shouldn't really work here since it is not בעידנא, meaning that the לא תעשה of breaking the bones is violated prior to the performance of the aseh. In such a situation we do not allow the aseh to push off the lo ta'aseh. Why would we need an extra pasuk by pesach sheini? Furthermore, the paradox is not absolute. One can fulfill the mitzvah of eating the marrow without breaking the bones. Since the paradox can be reconciled by using a coal to burn through the bone rather than breaking it, it is considered אפשר לקיים שניהם so we don't allow the aseh to push off the lo ta'aseh. In short, why does the braisa claim to warrant an extra pasuk based on the rule of עשה דוחה ל"ת. Since it is not בעידנא and it is אפשר לקיים שניהם, there are two reasons for us not to apply the concept of עשה דוחה לא תעשה to this case? Tosafos only answers the second question by saying that if the problem of the coal is because it will burn through some of the marrow and be a violation of הפסד קדשים, it is not a possibility and therefore is considered אי אפשר לקיים שניהם. However, the first question of Tosafos still remains?
I would suggest that the braisa never meant to apply the technical concept of עשה דוחה לא תעשה. The braisa is actually suggesting that due to the inherent contradiction between the mitzvah of eating the meat and marrow, and the issur of breaking the bones, we should limit the issur to only apply to bones that have no marrow. This is not applying the concept of עשה דוחה לא תעשה because that concept does not limit the lo ta'seh, rather it overrides it. The braisa is only saying that conceptually one should not find it strange that the mitzvah of eating the korban pesach would prevail over the issur to break the bones, forcing us to limit the issur, because we always find that an aseh pushes off a lo ta'aseh. The braisa doesn't met to apply the technical concept, just draw a conceptual parallel to justify limiting the issur to bones with no marrow.
Rashi also asks the second question of Tosafos. Why does the gemara consider there to be an absolute contradiction between the mitzvah to eat the korban pesach and the issur to break the bones, they can both be fulfilled by using a coal to burn through the bone? Rashi answers - דלא מצריך ליה קרא מילתא דאתי בה לידי תקלה דלמא פקע, the torah wouldn't require doing something that can cause the breaking of the bone. At first glance, Rashi is very difficult to understand. The gemara on 84b was very clear that this concern of דלמא פקע is only Rabbinic in nature, but on a Torah level using a coal is a good option to access the marrow without violation. How can Rashi say that the Torah itself rejects this option, since the entire concern is only Rabbinic? I would suggest that Rashi is not referring to the Rabbinic prohibition of using a coal to burn through out of concern that it will cause a crack. Even if the Rabbonon never created such a prohibition, Rashi would make sense. Rashi is saying that the Torah would not include the marrow in the mitzvah and obligation to eat korban pesach if there were a significant chance that by doing the mitzvah one would be in violation of an issur. Even if it were permissible m'dorayas and even m'drabonon to use a coal to burn through the bone, since there is a concern that it will break the bone, albeit a small concern, the Torah would not require it to be done to fulfill the mitzvah. In other words, Rashi is saying that we never find that the Torah would obligate a mitzvah at the risk of the violation of an issur. This is a fascinating yesod!