In my experience helping DMs balance encounters, there are two main reasons for why this happens (maybe one might apply to your case).
Either the DM applied the encounter XP multiplier incorrectly, by including all monsters when determining it, and thus vastly overestimated the adjusted XP for the encounter (this is super common with online encounter calculators, since they always include all monsters). Or PCs were able to set up an effective "kill box" for the encounter, where they could deals large amounts of damage to enemies while those enemies couldn't attack them effectively.
In the first case, the problem is fixable, at least to an extent, through changing the encounter building rules. The encounter XP multiplier shown in the DMG assumes the monsters have similar CR (or more specifically, similar XP values). When that assumption fails to be true it gives increasingly inaccurate results. The alternative rules in XGtE get around this by "recentering" the math around 1 monster / PC, rather than 1 monster / party of 4 PCs.
In the second, I don't think the problem is fixable from an encounter building rules perspective. The fundamental assumption around encounter balancing is that the PCs and the monsters can meaningfully interact with each other during the encounter. If the PCs manage to get themselves in a position where they break that symmetry then all of the math used in encounter balancing goes out the window. I think the best the rules can do in this case is to be clear on what their core assumptions are and when they break down.
I'd also like to point out, for the first case, there's a good mathematical check a DM can make to see if they've likely applied the encounter multiplier incorrectly. You can estimate the maximum possible difficulty of an encounter by taking the square root of every monster's XP, add them up, and then square the resulting total. This represents, roughly, how much XP an encounter would be worth if the PCs distributed their damage evenly across all combatants, waiting to the very last moment before killing them all at once (an extremely sub-optimal tactic). If the adjusted XP total for the encounter ever exceeds this value, something's gone wrong with the encounter's XP multiplier.