There was a thread a couple days ago and there seem to be issues with destinations where DL only has seasonal service (like PRG, GVA, ZRH, etc.).

Delta and PRG next year

Delta.com generally only shows 100% DL coded flight options, but there seems to be issue with generating fares that include DL coded flights on last hop. Suspect it is a combination of fare rule issues and delta.com not showing fares that include partner coded flights.

You can see below that all DL fare options below showing on ITA Matrix for DAY-GVA involve partner coded flights on last hop even though there are DL codeshare flight numbers assigned to these partner flights. Since there are no 100% DL coded options available, delta.com is not showing anything.