"We started the second half with 10 men and I was wondering where he was," said Jones.
"If I'd had an experienced centre-forward as a substitute, he'd have been off.
"Jay was superb, but he let himself down in that one incident. He had an excellent first half and a really good second half.
"We have a kick-off routine and because Jay was missing we couldn't do it. I know where he was - nothing escapes me.
"One lapse could have cost us something and that's what we are trying to cut out."
Derby scored within two mins of the re-start so Jones I guess was right to be upset with Bothroyd for upsetting the routine - although the defending to allow Derby to score was pretty bad.