The official sent off two City players and that sparked a furious outburst from Jones. Since then the FAW have overturned the red card issued to Darren Purse meaning he can face Palace on Saturday.
"I think Dave is only saying what a lot of us managers are thinking ourselves deep down and would like to say ourselves," Warnock told Wales Online.
"Dave will get into trouble for them, but at times you do have to make a comment.
"These kind of decisions can affect a manager's career. Look at Aidy Boothroyd at Watford. We have that 'goal that never was' at Reading and a few weeks on Aidy is out of a job. There is a link there.
"I believe the FA's Respect campaign has backfired. I think it is actually causing them to come out with even stranger decisions than they were before the campaign started."
Of the controversy surrounding Saturday's game between QPR and City, Warnock said: "He is a referee I am familiar with. At QPR last season he sent me to the stands."
But Warnock did smile at the way the FAW had let Purse off the red card given to him by Probert.
The decision, the second time the FAW have cleared Purse this year, means the Cardiff skipper is free to play against Warnock's Palace.
"From here on in, I'm going to appeal to the FAW myself," Warnock said with a laugh.