Stewart left late in the first quarter after he suffered an aggravation of the hamstring injury that kept him out for the Dec. 20 loss at Pittsburgh.
He appeared to know what had happened immediately after his last play, when he broke up a deep pass for Chargers TE Antonio Gates, but quickly retreated to the bench, throwing his helmet in frustration.
Harris played through a shoulder injury that left him "pretty sore" Monday morning, Kubiak said.
"I'm hurting, man," Harris said after Sunday's game. "I was hurt pretty much the whole game, but I'll be good.
"I need the bye week," he added. "At first, I was feeling great until [Sunday]."
Ware was limited to 27 snaps Sunday because of the knee problem, which came in his fourth game back from a back injury that sidelined him from the second half of the Week 9 loss at Indianapolis through Week 13.
"So Brandon was ready to go. He worked hard to go. We did make a decision early in the game -- and we were playing a lot of dime, so it was a little bit different. I don't think we went backwards. We've got a chance right now to get him a little bit more healthy. We've got some time on our hands, so he'll fall into that category [with] probably about five or six guys on our team."
Kubiak said that he thought "everything was okay" with quarterback
"He played under center, he played in the [shot]gun," Kubiak said. "I wouldn't say we went in saying we would sit in the gun [if Manning played], it was just, 'Hey, we're ready to go, let's go play.' So I think he's okay."
Kubiak said the difference with Manning last week compared with previous weeks of work in his rehabilitation was in the feedback the quarterback gave him.
"I just think the last 10 days were different -- much different," Kubiak said.
Emergency Room Care/ Denver ERs
HealthONE has 12 full-service emergency departments -- seven at our hospitals and five free-standing ERs. These include a Level I Trauma Center (adult and pediatric) at Swedish Medical Center; Level II Trauma Center at The Medical Center of Aurora; and Level III Trauma Center at Sky Ridge Medical Center. AIRLIFE-DENVER is our air medical transport serving facilities in an eight-state region.
The Medical Center of Aurora
Saddle Rock ER
Centennial Medical Plaza
North Suburban Medical Center
North Suburban Northeast ER
North Suburban Northwest ER
Presbyterian/ St. Luke's Medical Center
Rocky Mountain Hospital for Children at P/SL
Rose Medical Center
Sky Ridge Medical Center
Swedish Medical Center
Swedish Southwest ER
The HealthONE System of Hospitals now offers you and your family convenient ways to find the closest HealthONE ER and average wait times. HealthONE's Fast LocatER is our mobile suite of tools that you can take with you on the go.
Text "ER" to 23000
Our 24/7 Emergency Rooms for adult and pediatric patients are prepared to serve your medical emergencies. Get our average ER Wait Times by texting "ER" to 23000. Standard message and data rates may apply.