Striker Chambers, 22, who has scored six goals in 22 appearances for the Minstermen this season, was replaced by Jamie Reed with 25 minutes left as York turned in a rare poor display to lose 3-0.
"What gets to me is Ashley Chambers gets booed off - clapped off, sorry - as he was brought off," fumed Mills in the wake of Saturday's 2-2 draw at Port Vale. "I find that amazing; a lad who's worked so hard for two years to help play a major part in getting this club back to where it is.
"It astounds me that he actually gets clapped off, a lad who everybody knows anyway finds it hard all through his career to have that confidence.
"He scored a goal at Wembley in the play-off final last season to enable us to even be sitting here and playing the likes of Port Vale - he needs applauding when he's on the field.
"I think it's disgraceful, actually. I know how hard it's been to get the club here in two years, this hasn't come easy and the fact we had a poor performance that day - in my opinion the only poor performance this season - makes it hard to understand."