What if you make a new paragraph style similar to the previous ligatures off and apply to the all Document
Post ID questions to the ID forum. This is forum about design, not InDesign.
In advanced mode you will see paragaph styles. If not go to Windows>styles>Paragraph style.....
or press F11 to call out Paragraph style window
Go to edit your basic paragraph style or any other paragraph style you have.
Under paragraph style options window> Basic Character formats> uncheck Ligatures.