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Ince, who was awarded man-of-the-match by the club sponsors, was brought off for Dion Conroy in the 76th minute which angered many of the Swindon supporters at the County Ground.
The on-loan Brighton midfielder was given a standing ovation by the home crowd while they were simultaneously booing Williams and chants of "you don't know what you're doing" were then aimed at the 35-year-old head coach who is back making pre-match tactics and on-pitch decisions after director of football Tim Sherwood relinquished the duty.
In his post-match press conference Williams cited the fact that Ince was on a booking and his fitness as reasons why he brought him off.
"I thought he was outstanding," Williams began.
"I appreciate the fans giving me some stick when he came off because that's a compliment to Rohan.
"I felt like he was tired. He hasn't trained fully, obviously with the court case (Ince was found not guilty of grevious bodily harm), he started to look tired (and) I felt the (second) booking was coming.
"I felt that there could be one clumsy challenge that leads to him being sent off and I don't think we would want to go into another game without him - I thought his performance was excellent.
"Again, I can understand the frustrations of the fans. I think I'm wrong if I don't take him off and he gets sent off and then I'm wrong if I do take him off and everyone thought he was playing so well so I get that and Rohan knows the decision and why."
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