There are two common circumstances that meet this description. Although these nearly-empty trays look suspicious, they are usually correct.

1. Your nearly-empty tray might be a 3-digit tray going to a nearby area served by your SCF. There is a special rule for 3-Digit/Scheme trays: “After all full trays are prepared, one less-than-full tray must be prepared for any remaining pieces for each 3-digit ZIP Code/scheme of SCF serving post office where mail is verified.”
2. Your nearly-empty tray might be a 5-digit carrier route tray for a ZIP Code where you do not have many pieces that qualify for carrier route rates. Although the U.S. Postal Service now allows 3-digit carrier route trays in some circumstances, that level of sortation is optional and Envelope Manager does not support it.