The Golden Eagles (13-2) outrebounded Drexel by 52-34, including a 22-6 advantage on the offensive end. The Dragons struggled shooting from the floor (38 percent) and made just 5 of 17 free throws (29 percent).
"We've scored less than  points our last four games," Flint said. "We've been shooting like this the last four games."
Trailing by just 31-28 at halftime, Drexel (8-5) managed only six points over the first 13 minutes, 17 seconds of the second half, as Southern Miss ran away to a 60-34 lead with 6:43 to play.
"With six minutes to go, my assistant said, 'Hey, you know we've got six points, right.' " Flint said. "But it wasn't a surprise [because] we played that way."
The Dragons lost for the third time in their last four games and dropped back-to-back games for the first time this season.
Sophomore forward Tavan Allen led the Dragons with 15 points, while senor guard Chris Fouch added 13 points.
Southern Miss guard Aaron Brown, a Temple transfer, led four Golden Eagles in double-figure scoring with 11 points, while forwards Michael Craig and Jeremiah Eason and guard Jerrold Brooks added 10 apiece.
Craig posted his third consecutive double-double, grabbing 11 rebounds.
"Our initial defense was fine," Flint said. "It was after that. Once they missed a shot, they went and got it. We just couldn't come up with a rebound."