AmazingMIDI apparently can only transcribe a single instrument …
"AmazingMIDI automatically transcribes music, converting WAV files into MIDI files. It can recognize > single-instrument > polyphonic music. It’s a powerful tool to help you to transcribe music, to practice musical instruments and to make MIDI files, and so on. "
So if you feed it a track with bass & lead & drums, (e.g.), it won’t be able to comprehend it : like trying to translate two people speaking at the same time.
You’d need to give it the bass-only track , then the lead-only track , if you have those tracks in isolation , or can create them.