Inaccurate Results:
Given the machine learning nature of the program, unsupervised runs of the system can increasingly make the resulting transcriptions inaccurate.
Manipulated Compositions:
The user may alter a composition's audio file (distorting, cutting, etc.) before inputting into the program which may go against the composer's intentions.
Have a regular check in on transcriptions outputted by the program for quality control.
Have the majority of machine learning take place before public release.
Make it apparent that no piece of sheet music provided by the program is a legitimate interpretation/copy of a work. It is merely a tool for personal use.