To waive penalty, please visit any loan. To do this, please login and visit Loans(left menu) >> View All Loans >> Pencil button. Then click on the Loan Terms tab. There click on Edit Loan button. After doing this, please go down the page and in the Manual Penalty (optional) section, click on Override System Generated Penalties?. Then put the amount in Manual Penalty Amount. You can also put 0 here to remove all system generated penalties. Screenshot attached.
Please note that if you do the above, system generated penalties will not be added for this loan in future. You will need to uncheck Override System Generated Penalties? and then system generated penalties will be added again.