Yes, some dyslexis like myself do. For example Pin and Pen both sound the same to me. I don't care how you try to pronounce them or with different accents. They are always the same.
If someone is using the wah-wah pedal with an electric guitar to change the timbre of a note, can you tell?
Is it really about sound? Or is it just that the "phonetic analyzer" isn't distinguishing the phonemes?
If you can consciously hear the acoustic difference in timbre, how can you then not use that to tell the words apart (even if slowly/inefficiently)? As in "I just heard something that may be pin or pen; now I have to concentrate on what I heard. Hmm, the vowel sounded like a band filter tuned toward a higher frequency so it must be pin, rather than pen."