The following contains spoilers for episode 1 of Loki on Disney Plus.
Loki is already messing with the rules of time in the MCU, but it's not as though something like this was unexpected, given the nature of the lead character. Already, the first episode shows off Loki's rebellious and chaotic nature, while also taking the time to explain how time travel - specifically in regards to the Time Variance Authority and their mission - works, both to Loki as well as to the viewer.
The only hitch is that the rules of time travel in the MCU have never been super clear. Avengers: Endgame was the film that really attempted to define the regulations around hurtling through time, but many fans were very confused by how timelines worked and how time travel was being implemented into the film. It was understood that messing with the timeline (such as by stealing Infinity Stones from their set place in time and space) would create diverging timelines that would mess with the multiverse, but that was supposedly rectified by Captain America's mission at the end of Endgame that involved him returning the Stones to where they were supposed to be. However, the existence of the TVA in Loki and their goal to keep the timeline clean complicates this whole plot, despite the show's attempts to explain it away.
Loki explicitly points out to the TVA that the Avengers intentionally messed with the timeline, and so in theory, they should be variants just like him, and the TVA should be going after them as well. However, Ravonna Renslayer (Gugu Mbatha-Raw) tells him that they are not variants because their actions were supposed to happen. It was always in the grand design of the universe that they would travel through time to retrieve the Infinity Stones and ultimately stop Thanos. This makes sense on the surface, because the TVA would likely have a vested interest in stopping Thanos as a threat, and would be fine with the Avengers messing with timelines a little bit, as long as they set them back to normal in the end.
However, Loki is quick to question who has the authority to dictate what is supposed to or not supposed to happen in the timeline. The answer is the Time Keepers, but Loki doesn't accept that they should have absolute ruling over every person's life and the way that they are allowed to affect the Sacred Timeline. This is a good point and is something that the show will hopefully explore in the future. Why was the Avengers' interference with the timeline meant to happen, while Loki's was not? Why do the TVA and the Time Keepers seemingly get to pick and choose who is allowed to change timelines?
This idea of what was "meant to happen" also calls into question Steve Rogers's decision at the end of Endgame to stay in the past and live the remainder of his life with Peggy Carter. While there are ways to justify the Avengers' use of time travel in Endgame (namely that they need to do it to save the world), the rules around Steve's choices are now more unclear. Was this also always meant to happen, and is this confirmation that Steve did not enter an alternate timeline with Peggy, as was previously thought, and actually went back to be with her in this timeline?
The entire point of the TVA is to preserve this singular timeline and prevent others from branching off of it, so unless they're also hunting down Steve (which doesn't seem to be the case) or they've just decided the rules don't apply to Captain America, the TVA has decided that Steve's choice was always meant to happen and he has always been with Peggy in this timeline.
However, this is complicated because it would mean that Peggy lied to him in Captain America: The Winter Soldier, knowing that they were always married and he just wasn't aware of it yet. Of more concern is the fact that it would mean that Sharon Carter should have recognized Steve as her uncle, making their kiss in Captain America: Civil War even more awkward than it already is. So unless Marvel is willing to defend this, it means that the TVA has decided to just let Steve create a new timeline with no consequences, which directly goes against their mission. Was this also always "meant to happen"?
Usually, the MCU is really good about planning out their stories well into the future, but the messiness of the time travel plotlines in Endgame is just creating further problems for the MCU to solve. Some of the things we've learned about time travel in Loki directly conflict with the rules to time travel we were given in Endgame. Hopefully, the show will be able to clear up some of these questions in the future, and perhaps acknowledge why the rules only seem to apply to some people, or else there are some really questionable things going on in the Carter family regarding Steve Rogers. Either way, the MCU needs to perhaps work harder on their continuity, especially if they're intent on exploring time travel and the multiverse in the future.