Noob question. Pickup wiring.

Is it possible for me to have wired a guitar with EMGs incorrectly, so that its out of phase with a bass guitar?

Does that even make sense or possible?

no. you're doing going to have phase issues from a different instrument. phase issues are from different sources picking up the same signal from the same source. i.e. snare mic having phase issue with snare in overheads, or snare mic on top and snare mic on bottom. basicly the waveforms "headbutt"