Sunderland could be without key trio for huge League One clash at Barnsley
Sunderland snatched a point late on at Adams Park, sub Watmore slamming home after Ryan Allsop spilled Grant Leadbitter's late effort from distance.
Watmore was then forced off with an ankle injury after Marcus Bean's late challenge, that tackle left Ross fuming.
Bean was shown his second yellow for the incident.
Flanagan, who had endured a difficult afternoon at the back for Sunderland alongside Jimmy Dunne, was forced off with a head injury.
If it was concussion then he wouldn't be able to play Barnsley on Tuesday evening, with Watmore also a big doubt and George Honeyman facing a three-game suspension after seeing red late on.
Alex Samuel caught Flanagan with a boot to the head during a collision.
Play was stopped for a length of time before Flanagan walked off the pitch.
On Watmore, Ross said: "First of all, I am really pleased for Duncan to get the goal after everything he has been through.
"He broke through a barrier with the goal in Checkatrade and to score such an important goal in a league game is another milestone.
"I wasn't too enamoured with the challenge, I thought it was a straight red not another yellow.
"He is a bit sore at the moment.
"But it is his ankle, a separate injury obviously but not brilliant for him after so long out."
And on Flanagan, Ross added: "I have not spoken to any of the medical staff yet, from his injury, I am not sure how he was on the pitch at the time.
"We have to assess it from a protocol side of things."
Wycombe Wanderers were physical from the off but Ross didn't think they were overly physical.
He added: "No, not really no. It was competitive. I said to the players at half time, you have two choices.
"Think that shouldn't happen or deal with it and give as good as you get.
"I have no issue, they make it tough. We have to deal with it as a team."
Sunderland are back in action on Tuesday night when they travel to promotion rivals Barnsley, who beat Accrington Stanley 2-0.