I can't be sure exactly what is going on because the screenshot isn't comprehensive. Would you be able to share a .twbx (packaged workbook) which replicates the issue? Or, at least, a more comprehensive screenshot that shows the axes of the waterfall charts and what the reference lines are set to (a constant, a percentage, etc.)
If you set the axes to the same fixed axis and set the reference line to a constant, they should match. But I can't be sure if that will work for you without seeing more.