All it took was a visit from Virginia Tech's stout defense to make those problems obvious for all to see.
Virginia Tech's defense shut down Georgia Tech's proud running game and the Hokies beat the error-prone Yellow Jackets 17-10 on Thursday night.
Georgia Tech (3-1, 2-1 Atlantic Coast Conference) had nine penalties - including six for false starts - and lost three turnovers.
Georgia Tech's fourth-ranked rushing offense was held to 129 yards - more than 200 yards below its average.
"It's been coming," Johnson said about the offense's struggles. "I've told you all along we're not very good with the option. We're terrible, in fact, and it showed. We're not going to throw the ball 24 times and win very many games. That's not us. We've got to be able to run the ball ... and we didn't do it."
Vad Lee completed only 7 of 24 passes for 144 yards with two interceptions while also losing a fumble.
"They had a good defensive scheme," Lee said of the Hokies (4-1, 1-0).
"Virginia Tech has always had good defense. For the most part we were killing ourselves with the penalties ... and you can't do that."
Lee said the loss showed the Yellow Jackets need more practice.
"We've just got to get better," Lee said. "I've got to do my part better. If anything on offense happens, I put it on me."
Logan Thomas overcame an abdominal strain to complete 19 of 25 passes for 221 yards, including a 21-yard touchdown pass to D.J. Coles. Thomas had 16 carries for 58 yards and a touchdown.
"I wasn't sure I was going to be able to make it through," Thomas said. "I wasn't able to practice pretty much all week."
Virginia Tech earned its fourth straight win in the rivalry that often decides the Coastal Division's representative in the ACC championship game. Virginia Tech (five) and Georgia Tech (three) are the only teams from the division to play in the championship game.
"It's frustrating but it's just one game in a big season," Georgia Tech defensive end Jeremiah Attaochu said. "We've got a lot of things in front of us that we can accomplish, and that includes an ACC Championship."
Georgia Tech made it to last year's ACC Championship Game despite losing at Virginia Tech.
David Sims scored on a run from the 2 in the third quarter for Georgia Tech's only touchdown.
Kyle Fuller had two tackles for losses and a forced fumble, Brandon Facyson intercepted a pass and had a forced fumble and fumble recovery and Derrick Hopkins had seven stops to lead a strong performance by the Hokies' defense.
Virginia Tech overcame a short practice week to find a defensive plan to contain Lee and the spread-option offense that was averaging 45.3 points per game.
"I think we're fortunate to have some veterans up front that have played against their offense a couple of times," Virginia Tech coach Frank Beamer said. "It's a rugged offense. You have to be rugged yourself to play it. You have to be very precise."
Led by Hopkins, the 311-pound defensive tackle, Virginia Tech stopped running back David Sims on back-to-back plays, including a fourth-and-2 run, midway through the fourth quarter.
Cody Journell was wide left on a 25-yard field goal for Virginia Tech with 5:37 remaining to keep Georgia Tech's hopes alive. Kendall Fuller intercepted Lee's fourth-down pass from near midfield with 1:06 remaining to clinch the win.
Georgia Tech trailed 14-3 at halftime before closing the gap with a 14-play drive that consumed more than 8 minutes of the third quarter.
Big plays of the drive were a 40-yard pass from Lee to Robert Godhigh and two Virginia Tech penalties that gave the Yellow Jackets first downs, including a fourth-and-1 offside call on linebacker Jack Tyler. On third down from the Virginia Tech 10, Hokies free safety Detrick Bonner was called for pass interference as he deflected a pass intended for DeAndre Smelter.
Journell's 39-yard field goal pushed the Virginia Tech lead to 17-10.
Thomas had a 5-yard touchdown run in the second quarter for a 14-0 lead. Thomas matched Tyrod Taylor's school record of 23 rushing touchdowns by a quarterback.
Georgia Tech's only points of the first half came on a 49-yard field goal by freshman Harrison Butker midway through the second quarter.
Georgia Tech, celebrating the 100th anniversary of Grant Field at Bobby Dodd Stadium, wore throwback jerseys from the 1950s and 1960s.
Virginia Tech unveiled new silver-blue Hokie Stone helmets and wore maroon jerseys and pants for the first time since playing Miami in 2009.