Yes they thought the real plane was an input then realised the facts. The exercise hadn't started yet. They weren't responsible for civilian planes in 2001.
NORAD is the joint U.S.-Canadian military organization responsible for monitoring and defending the airspace over North America. Long-standing operating procedures at NORAD, for dealing with airliners that have gone off-course or been hijacked, were not followed on 9/11. Each of the four flights involved in the 9/11 attacks should have been intercepted when they lost radio contact, deviated from their course, or turned off their transponders.[2]
[2] Bob Arnot, What Was Needed to Halt the Attacks?: Cockpit security, quick response not in evidence Tuesday, MSNBC, September 12, 2001,
The procedures for interception were automatic and required no special orders to implement. Through these procedures, interceptor jets had been scrambled 129 times in the year 2000 and 67 times in the year prior to June 2001. A 1994 government report stated — “Overall, during the past four years, NORAD’s alert fighters took off to intercept aircraft (referred to as scrambled) 1,518 times, or an average of 15 times per site per year. Of these incidents, the number of suspected drug smuggling aircraft averaged … less than 7 percent of all of the alert sites’ total activity. The remaining activity generally involved visually inspecting unidentified aircraft and assisting aircraft in distress.”[3]
[3] United States General Accounting Office, Continental Air Defense: A Dedicated Force Is No Longer Needed, May 3, 1994
https://digwithin.net/2013/01/12/eberhart/