It's the same foot that Thomas suffered the Lisfranc injury on last summer, causing him to miss the season.
"It's a concern because it's the same foot," Gruden said. "It's just sore. It's still bothering him. You can see a little bit that it looks like it's bothering him. We've got to get it fixed because he's a good player and we need to make sure he's healthy when he's ready to play."
Thomas has worked as the Redskins' No. 2 strong safety this summer, behind Brandon Meriweather. But with Meriweather's penchant for drawing fines and possible suspensions for illegal hits, the Redskins need a solid backup. Meriweather was flagged for a personal foul on a hit vs. Baltimore Saturday.
Thomas also missed two weeks of training camp with a strained hamstring.
Also on the injury report:
Tight end Jordan Reed sprained his thumb against Baltimore and did not practice. Gruden said he would be fine for the season opener vs. Houston.
Rookie tackle Morgan Moses practiced after suffering a sprained right knee against Baltimore.
Linebacker Brian Orakpo sat out with a sprained ankle.
Linebacker Darryl Sharpton, who has a high ankle sprain, went through some individual drills but Gruden said he was "very limited" in practice.
Corner Tracy Porter practiced, but Gruden said he might have re-injured his hamstring. "He looked like he wasn't quite himself," Gruden said.