The National Weather Service had not issued a tornado warning yet when the EF-0 storm hit around 5:41 a.m. near 95th Street and Route 59 Saturday morning.
But a tornado warning was issued shortly afterward, which should have triggered the sirens. It did not.
The city said it's looking into this situation with "extreme urgency."
The majority of the damage reported was along the Route 59 corridor from approximately White Eagle Drive south past Hassert Boulevard, NWS said.
Isolated reports of storm damage, mainly damaged trees, were made throughout south Naperville. Roof damage and multiple gas leaks in a commercial building were also reported, authorities said. Additional damage included a dozen roads blocked by fallen trees or limbs, minor flooding issues and a power outage in the area of Washington Street and Gartner Road caused by fallen tree branches.