With broad swaths of the country in the throes of a highly active tornado season, federal forecasters are wrestling with the gaps in their knowledge of how tornadoes form.

The science community now believes tornadoes most likely build from the ground up and not from a storm cloud down, potentially making them harder to spot via radar early in the formation process. But scientists still struggle to say with certainty when and where a tornado will form, or why some storms spawn them and neighboring storms don’t.

“Sometimes...