Most fans agree that Dragon Ball Super is a worthy successor to Dragon Ball Z, even if it's not perfect. It's certainly better regarded than Dragon Ball GT, the original successor series to Z, which has a rather poor reputation among fans. However, GT's existence is still considered canon by the makers of Dragon Ball at Toei, and that causes some major issues when trying to squeeze Dragon Ball Super into the timeline.
Dragon Ball Super is ostensibly set in between the end of the Majin Buu Saga of Dragon Ball Z and the flash-forward to ten years in the future which makes up the series' epilogue. A ten-year window seems like it would provide plenty of room to avoid continuity issues, but as Dragon Ball Super has continued, it has crept closer and closer to that timeframe, with Dragon Ball Super: Super Hero supposedly set just one year before the epilogue of Dragon Ball Z. With Super still continuing on, it represents a major issue in regards to continuity, and it's a difficult one to reconcile.
Dragon Ball Super Often Contradicts Z and GT
Super's Story Advancement Outright Contradicts Older Series
Dragon Ball Super has seen Goku and Vegeta obtain new levels of power that would've been almost unimaginable in the Dragon Ball Z days, fighting on the level of gods and training under an Angel and the God of Destruction himself, Beerus. Needless to say, none of this is reflected in GT, which is ostensibly set after Super even though it was created before. Fans revisiting GT now often have to ask themselves, "why isn't Goku or Vegeta using Ultra Instinct/Super Saiyan Blue/etc. to solve this problem?" and the series really doesn't offer much of a solution.
As the latest addition, it's up to Super to make sure that it fits into previous continuity, and that includes the series which follows it as much as the one that preceded it. But the problems go further than just the absence of the new forms introduced in Super from GT. Vegeta's character, for example, has developed quite a lot over the course of Dragon Ball Super, but that character growth isn't reflected in GT at all, as he's exactly the same as he is at the end of Dragon Ball Z.
If the problems were only with Dragon Ball GT, that could easily be dealt with by declaring GT non-canonical, which many fans already consider to be the case anyway. However, Super isn't consistent with the epilogue of Dragon Ball Z either; most obviously, Bulma says in the penultimate chapter of the manga that they haven't seen Goku in five years, something that's clearly not true in Super. Vegeta also acts as if he hasn't seen Goku in ages, when the reality, according to Super, is that they've been training together for years now.
Dragon Ball Super Is Running Out Of Time To Resolve These Conflicts
Both In-universe and out, Super Doesn't Have Much Time to Address The Problem
With Super Hero having moved the timeframe of Super up to just one year before the epilogue of Z, there's very little opportunity for the series to correct these continuity conflicts. The Super manga is currently on hiatus, but it's widely believed that when it returns, that will be Dragon Ball Super's final arc. That means that if these problems are going to be dealt with, the next arc will have to be the one to do that, and it's looking highly unlikely that this will be the case.
Super's conflicts with Z's epilogue can be explained somewhat; Goku has indeed spent several arcs of Super in space at this point, including the bulk of the Galactic Patrol Prisoner Saga and the Granolah the Survivor Saga, and he only returns to Earth momentarily to pick up Gohan in the post-Super Hero chapter. Perhaps Goku and Vegeta really have been primarily offworld for five years of in-universe time, and Goku simply didn't encounter Bulma on any of his return trips to Earth. It would hardly be out of character for Goku to forget to say hi to his friends, after all.
The conflicts with GT are much bigger and harder to solve, however. It's simply impossible that Goku and/or Vegeta wouldn't at least mention their godly forms, even if they weren't an option for some reason. There's also the absence of Beerus, Whis, and other Super characters who would presumably still be around during the time of GT. For example, with Broly now as an ally, where was he during the various crises that they faced during GT?
Can Dragon Ball Super Fix Its Continuity Errors, Or Should It Just Be Ruled Non-Canon?
It's Not Impossible to Fix these Problems, but Changes to Canon May Be Necessary
With Dragon Ball Super's extreme popularity, it seems like there's almost no way that it would ever be deemed non-canonical. As something which was guided by Akira Toriyama, Dragon Ball Super has a far greater claim to being canon than GT does, so if anything, GT is the one that should be declared non-canonical when the two conflict. Toei seems extremely reluctant to do this for whatever reason, but with Super getting closer and closer to the time that GT is set, it's a problem that they'll have to address sooner or later.
That still leaves the problem of Dragon Ball Z's epilogue, however. As part of Z, it would be difficult to simply declare the epilogue itself as non-canonical, even if that's the simplest solution. Perhaps Dragon Ball Super can show a new version of the events seen in Z's epilogue, one more consistent with the story of Super, thus offering more of a retcon solution than just ditching the Z epilogue entirely. With the addition of Dragon Ball Daima to the mix soon, there could be even more continuity problems to arise depending on precisely when that series is set.
Dragon Ball Super's continuity issues are certainly a headache to deal with, so hopefully the powers that be will make a decision with regard to Dragon Ball continuity soon.