Indeed. And it's often not even the adjustment of the subs. My bass is excellent and has been lauded by audiophile friends who visited. Yet this week I moved my main speakers 2 inches further back and 2 inches from the sidewalls, in order to (successfully) remove some slight distortions in mids and highs, due to speaker/room interaction, which had been starting to bother me. Turns out, bass, including low bass, also becomes even better. Before the move of the main speakers I had been admiring the sound of the stand up bass solo in a track with the Benny Green trio. Yet a few of the low notes were just slightly fat. Turning down the sub from its relatively high setting on that track by a little solved the issue. To my astonishment, after the speaker move, and with the old higher sub volume setting, the bass on that solo is now completely even throughout the range, and tight also in the low notes (yet still with the roundness of plucked stand up bass).
Here's the kicker: I have two-way monitors and they do not reproduce low bass at all on this solo. Yet the leading edge of their bass before the speaker move still made the low bass contribution of the subs sound just ever so slightly bloated. Needless to say, it is now absolutely impossible to tell that a monitor/sub combo is reproducing that bass solo, rather than a single speaker (on most other material it was impossible to tell even before the speaker move).
So when you think it's the subs or their adjustment that are the problem when you hear an anomaly, think again. It may be a problem with the setup of your main speakers instead, and one that you might not hear without the subs playing.