Yeah that's a cymbal hit over and over
"Tee tee tee tee tee"
And a phase shifter is like turning down the bass and turning up the treble at the same time, then reversed, over and over in a cycle. It makes a "sheeeeee-ooooooo-eeeee-oooo" sound.
You're saying the initial cymbal hit is producing a note, like a piano or guitar would, that is unpleasant and out of key with the rest of the piece, not to mention very different from the SNES version?
I'll load up a save and see if my emu knows what you're talking about.
Edit: I hear it. The emulator I used was the mGBA core on Retroarch version 1.3.2.
It is making a noise that is not present in the SNES version so far as I know, yes.