In Avengers: Endgame, the heroes of the Marvel Cinematic Universe found the world in its darkest hour after half of all life was destroyed during the events of Avengers: Infinity War. After busting in on Thanos' retirement farm to make him undo the damage from the previous films the Avengers quickly discovered he couldn't. He used the Infinity Stones to destroy the Infinity Stones -- except he shouldn't have been able to.
The comics make the matter pretty clear cut, stating the the Infinity Gems cannot destroy themselves. When Reed Richards assembles all of them together in the Infinity Gauntlet he tries to destroy them due to the belief that no one person should wield such omnipotence. However, he finds the task simply impossible. The Illuminati are forced to scatter and hide the stones instead. But the MCU blew right past this plot point.
While critics could claim the logic of the MCU is different from that of the comics, the problem only reemerges when taking the MCU's own logic at face value. As explained various times throughout the series, the Stones embody the infinite energies that formed the universe. The Collector refers to them as six singularities. And even a basic understanding of physics entails an understanding that energy can be neither created nor destroyed.
With the Infinity Stones, each ingot essentially represents an infinite amount of energy that was impossibly destroyed by Thanos' second snap. The film pays lip service to the power involved as the attempt nearly kills Thanos, leaving the arm wearing the Gauntlet withered after he does the deed. However, this fails to address just what happened to such unending sources of energy.
It would make more sense for the energy to be released and go elsewhere, free for the Celestials or the Elders of the Universe or anyone else to pick up at their leisure. Rather than pursuing this possibility, however, the Avengers instead throw up their hands at the impossibility of undoing Thanos' first snap and then undertake a convoluted time heist. It would almost be more logical if the Stones' destruction reversed the initial Snap than for it to simply obliterate all the energy they contain.
What's worse, Endgame itself recognizes the importance of preserving the Stones within a given timeline. When Bruce Banner visits the Ancient One during the Battle of New York and breaks down the Avengers' time heist plan, she explains how critical it is that the Stones are returned to their proper place in time. If a single stone remains out of place, an entire timeline becomes vulnerable and aberrant. And yet the destruction of all of the stones takes place before and after this explanation without addressing the elephant in the room.
What state is the main MCU timeline left in without any of the Infinity Stones if those Stones are supposedly what guard it from some existential threat? There is little doubt that the upcoming sequel Doctor Strange and the Multiverse of Madness will explore the implications of multiple realities, and the Disney+ series Loki will likely follow the Asgardian villain's journey with the Space Stone in his own reality. However, as of yet there is no explanation on the table for what will happen in the main timeline.
The lack of Infinity Stones could make the main timeline vulnerable to manipulation. Much of the speculation surrounding the upcoming Disney+ show WandaVision suggests that Scarlet Witch will unleash her reality-altering powers in ways that threaten the entire universe, as she did in the comics. Were those powers unleashed in the world of the MCU, existence itself could be too fragile to take such a blow.
The issue with the Infinity Stones would also be addressed through the Elders of the Universe already introduced in the MCU: the Collector and the Grandmaster. In the comics, these characters are brothers and hail from the time of the Big Bang, which would make them of a similar age to the Infinity Stones themselves. While the Grandmaster did not seem to care for much besides gladiatorial games, the Collector was obsessed with the Stones in Guardians of the Galaxy.
The fact remains that until the MCU addresses the issue with the destruction of the Infinity Stones, it will remain a plot hole. It has the potential to be serve future plotlines rather than contradict them, but without further explanation, fans are left to concoct theories and speculate about possibilities on their own. In that way, the results could be infinite.