Referee Jonathan Moss booked Bothroyd for diving in the 75th minute of the 2-1 loss at Nottingham Forest.
Jones revealed the official had spoken to him at half-time about Bothroyd.
"The referee called me in at half-time. It's the second time referees have said to me that they're not going to give free-kicks against him," Jones said.
"They feel he's going down too easy. If it's a foul it's a foul, it's as simple as that.
"Because it's a certain player they can't be going through the game thinking 'hang on, is he going down too easy' or whatever.
"To actually call you in and tell you that 'look, we're monitoring the situation with Jay' tells you that they're watching for things and that's not right.
"You give the foul if it's a foul. There's one incident where the lad's got his hands round his [Bothroyd's] neck and pulls him down and [the referee] waves play on.
"I'm not saying that they're getting every one right and wrong but really you've got to go on what you see, not what you think he's trying to do.
"That's something that they're trying to pre-empt and you can't pre-empt things like that, if it's a foul it's a foul and you've got to give what you see sometimes."
Bothroyd is Cardiff's leading scorer this season with 17 goals and earned a first England cap this season in the friendly against France.
But the former Wolves frontman, plus midfielders Chris Burke and Adam Matthews are out of contract at the end of the season.
Jones revealed that at this point he does not expect any of the trio to recommit themselves to Cardiff, although he remains hopeful that something could be agreed once the season ends.
"We've put the contracts to them. Their agents decided they wanted to run it until the end of the season and see what happens," Jones said.
"We don't know what else we can do. You go as far as you can and then it's down to the player and the agent.
"There hasn't been a problem with it, it hasn't made them play any better or any worse.
"At the end of the day they'll have a decision which is fine, I haven't got a problem with it because it's their prerogative to do that.
"We've offered the best that the club feel they can give and if that's not good enough then I haven't got a problem with that and they've got to find it somewhere else.
"I think sometimes you get bogged down in negotiations and they go on for ever and ever, and I've always believed that you make the best offer and if that's it then that's it and then you have a decision to make.
"But you keep throwing and throwing and throwing [money] at it and then you end up in all sorts of trouble like this club's been in in past years."
After losing ground in the Championship promotion race to Forest, the Bluebirds will look to bounce back on Tuesday night against another promotion rival when Leicester City come to the Cardiff City Stadium.
Source: BBC Sport
Source: BBC Sport