The chord I was playing was actually a CMajor with the bass playing E. Logic doesn't really pick that, though
That's simply the first inversion of a C Major chord - 3rd (E) as the root.
Bizarre that Logic doesn't understand that and complicates it to what you saw: E no 3 flat3/sharp5
You should file a bug report...
Since I'm actually playing the CMaj triad AND the E an octave below, it's not assuming it as C. If I don't play the E as part of the triad, then it assumes it's C.
I think it's probably just a way to make you think and see that you're not actually playing a "normal" C chord.
For example, on a piano, an inversion sounds like a C, but if you have a guitar and a bass, where the guitar plays the C chord and the bass plays E, then it sounds different.
That's why I always debate when some people bring theory to explain certain things (this is not the case, of course), because each instrument and the way two different instruments work and sound together, can change how theory is applied. Just because 1+1=2, doesn't mean that it makes sense all the time, depending on the situation. Hope it makes sense
(stupid) example: 1 divided by 2 = 0.5, correct?
Well if I cut an orange in half, now I get 2 halves, so we can write it as 1 divided by 2 = 2
It all depends on the context and what the output is and means. In this case of music, it's subjective depending on the instruments and how they relate