I don't think it's an out of tune guitar or wrong bass note; I think it's just the unique harmony. From what I could hear, the guitars are basically playing this chord progression in the intro:
F#maj7 - F#m7b5 - G#m7/F# - F#
Whereas the bass is playing:
F# (then high F#) - E - C# A - F#
I think that's right, but I didn't listen long so I'm not positive. The E note would technically work over the F#m7b5, but it tends to highlight the dissonant aug 5th interval between E and C. Or maybe it's the C# A beneath the G#m7 chord that's bugging you. While that technically clashes, it just kind of comes off as a bluesy embellishment to me and therefore works.
To me, the first "oddity" that struck me was the second chord (F#m7b5), but I got used to it eventually.
Anyway.... Yeah cool tune, well performed and some cool things going on. Bass may be just a tad loud. It's pretty up front. But other than that, it sounds pretty nice to me. Good job!