Sometimes, when a tenant is trying to make a payment online, they may want to make only a partial payment and not the full payment. Through your policies, you can control that setting.
You can either decide to enforce full payments only or change the setting to allow tenant to make a payment for any amount.
You can click on Administration-->policies-->Portal--Resident. Click on Organization and then click on the tab details.
You can then click edit and make appropriate changes.