Warning: Spoilers for Dragon Ball Daima, episode #18 ahead.Dragon Ball Daima may seem to have created a continuity issue with Dragon Ball Super by having Goku go Super Saiyan 4 early, but there's actually a perfectly logical explanation already built into the series. The answer lies with the one who helped Goku unlock this power in the first place: the Namekian, Neva.
In Dragon Ball Super, Goku mostly uses the Super Saiyan God form and its derivative, Super Saiyan Blue. However, there is a brief period before he obtains this ability, namely in the Beerus story arc, where Goku is seen battling in his classic transformations. At this time, which should be after Daima is set, Goku is only able to top out his transformation at Super Saiyan 3, and never uses Super Saiyan 4 against Beerus, despite having achieved the form before canonically, according to Daima. So why didn't Goku use Super Saiyan 4, and how does Daima offer an answer?
Quick Links
Dragon Ball Daima Unlocks Super Saiyan 4 Magically
Neva's Magic May Be the Answer to Goku's Transformation Problem
In Dragon Ball Daima, Goku is given access to the Super Saiyan 4 form after Neva performs a ritual on him, which seems to help him unlock that potential and achieve the new form. It's quite possible, if not likely, that Neva was the only reason Goku was able to access Super Saiyan 4 at this point in his training. The fact that Goku magically regrows his tail (and magically loses it again when Gomah reverts him to his base state) suggests that the Super Saiyan 4 transformation seen in Daima was magically assisted, and that it might otherwise be a bit outside of Goku's reach at this point in time.
While the ritual does seem similar to the potential unlock that Gohan undergoes from Guru on Namek, it may be that this is a slightly different version of the ritual, one designed to bring out more power on a less permanent basis. So far, Goku hasn't shown an ability to return to the Super Saiyan 4 state after being knocked out of it, so it may well be that Goku is only capable of attaining it with magical assistance from Neva, rather than having it unlocked for him at all times. That would explain why Goku didn't use it against Beerus--he wasn't capable of returning to that form with Neva's help, at least for now.
Would Super Saiyan 4 Have Even Helped Against Beerus?
The New Form May Not Have Done Much to Slow Down Beerus
The next question that one has to wonder is whether Super Saiyan 4 versus Beerus would've significantly changed the course of events. It seems unlikely that even Super Saiyan 4 would've had a substantial impact on the initial outcome of Goku versus Beerus. Goku may have been able to hold out a little longer against Beerus with Super Saiyan 4 than he did without it, but the fact of the matter is that without God Ki, Goku just didn't pose much of a threat to Beerus. It's only once he obtained Super Saiyan God and began fighting in that form that he provided much challenge to the God of Destruction.
As such, it doesn't matter too much whether Goku could transform further than Super Saiyan 3 or not; it simply wouldn't be enough to turn the tables on that particular fight. With Super Saiyan God and its associated God Ki at his disposal from this point forward, there's no reason Goku would even attempt to use Super Saiyan 4 again, especially once they've discovered Super Saiyan Blue. From Goku's perspective, Super Saiyan 4 would almost be more of an anomaly that cropped up one time than a form that he gained regular access to.

I Can't Believe It, But Dragon Ball Daima's New Villain Is Stronger Than Super Saiyan 4
Dragon Ball Daima has returned Super Saiyan 4 to its canon status, but the anime's main villain has already shown the form won't be enough.
Of course, there's always the possibility that Super Saiyan 4 could come back again in the Dragon Ball Super manga, now that it's firmly established in canon. Knowing Goku, he wouldn't be satisfied to leave such a transformation a mystery, and might have pursued it anyway just to prove that he could. Goku attaining Super Saiyan 4 does potentially open the door for other characters, such as Broly, getting the transformation as well, if he can replicate it and teach it to them.
While Goku's access to Super Saiyan 4 may be contingent on Neva's involvement for now, it doesn't have to stay that way forever; just long enough that he couldn't use it against Beerus a few months later. Super Saiyan 4 may yet be seen again some day, thanks to Dragon Ball Daima.