Dave Jones said: "At the end of the day it's probably our worst performance of the season.
"That's taking nothing away from Watford, but I think there were too many bodies out there that shouldn't have been.
"Even on the bench, it's kids and two of the players shouldn't have even been sitting on the bench but that's all we've got until we can strengthen and we're trying to get to that stage."
Whittingham's sopening goal looked to have put the visitors in control but Watford rallied well to dominate the game.
Jones added: "We were well beaten. We didn't look like we could raise a canter and even when we got our noses in front we didn't take the gift.
"Maybe, just maybe, everything just caught up with them.
"Probably the best move of keeping the ball got us the goal but there was no real tempo in it, there was no sharpness in it, it was just a bit of keep possession and work our way forward, but I didn't see any drive whatsoever."
In contrast, Watford manager Malky Mackay was delighted with his side's performance.
He said: "I think that's our best performance of the season. We've had a couple of good results away from home but I think that was a complete performance.
"Missing a penalty and then going a goal down can sometimes knock confidence and I think it's great to see the younger guys are learning from past experiences and growing.
"There wasn't a real period in the game where Cardiff dominated us and all over the pitch, in every position, we had players who were nine out of 10 and that makes a huge difference."