I've found most of my guitars have somewhat of a dead spot, often between the 10th and 14th frets, usually on the G string but sometimes on the B. But there are a combination of factors that cause it to be more or less noticeable. Mine usually show up more with gain, almost like a secondary and slightly out of tune frequency that fights the note, often can't hear it at all clean. Believe it or not, the guitar it shows up on most often is also my dearest one, the 594. The good news is, it goes away when turning the tone knob down to about 5 or below, and when I'm playing with enough gain to notice the issue, turning the tone knobs down like that on the 594 is pretty much indistinguishable in sound. The 594 is the brightest sounding of my guitars, my theory is it has to do with high frequency overtones, which is why it happens on the 594, and goes away when turning the tone knob down. The 594 pickups and electronics, fortunately, are tuned so that the body and "push" of the note aren't lost at all when the tone knob is turned down. The sound still fills up with harmonics from the clipping, it just doesn't have that "beat" frequency anymore.
I think it also has to do with imperfections of having a plain 3rd/G string, mass and tension in combination with how short the string is getting around the 12th fret and above, and maybe that carries over to the B string, too. There's some interesting info out there on it, some guys will go to a wound third to get away from it.
Personally, I'm starting to see it more as a guitar being "alive" enough sonically to display the slightly unfortunate idiosyncrasies of guitar string science, rather than a problem with the guitar itself.