We currently do not have a way to delete a custom fact on the program itself, so you will need to do this in your project.cfg file.
To delete a custom fact that you made in your project in Family Tree Builder, first close Family Tree Builder.
Then please go to browse your files on your computer. Go into Documents > MyHeritage > Project folder (same as the family tree name) > cfg and open the file project.cfg with Notepad. There you will see a line with the custom fact. Remove it, and save the file.