I think your idea is definitely reasonable: an emphasis in the treble part of any sound will tend to emphasize higher partials which could throw off your transcription. This is vastly more likely to only cause you to be incorrect about the actual octave of performance, although I see no reason—at least theoretically—that it couldn’t even potentially lead you to be off by a fifth.
The guitar would most likely have a treble emphasis either due to filtering or simply using the bridge pickup. It’s important to add that not only will these things provide an emphasis on higher harmonic partials, but perhaps even more significantly could emphasize inharmonic partials as well. These are partials that are not integer multiples of the fundamental, and they can throw a transcription off as well. An extreme example would be tubular bells: they have a spectrum that includes so many inharmonic elements that people often disagree about what octave the note is actually in. Some people will even tell you that you should write for chimes as if they transpose an octave lower than they are notated. Guitar tone is certainly more harmonic than bell tone, but, especially during the sound’s attack, there are still a substantial number of inharmonic partials. These would be emphasized at the bridge pickup and/or by any hipass filtering.
The best thing you can do, I think, it to try to learn enough about guitar performance techniques that you can judge the most likely interpretation. Study scores and professional transcriptions in order to get a better sense of what octave choices tend to happen in various circumstances.