The former Greece international has collected 11 bookings in the Premier League so far this term, with only Bournemouth midfielder Jefferson Lerma picking up as many.
Holebas has also averaged 11 yellow cards over the last two campaigns at Vicarage Road.
The 34-year-old is likely to line up against Wolves at Wembley on Sunday afternoon as the Hornets aim to secure their place in only their second FA Cup final and first since 1984.
"I don't get why people are so focused on yellow cards," he said.
"If you make a tackle and you start moaning it is emotional – that is football and that is what we're living for.
"It doesn't annoy me. It's just a yellow card, I don't know why there is such a big deal about it. If I get 20 (bookings) I get 20, that's it.
"The decisions sometimes from the referee, I don't understand it. One guy gives it for saying something, another for a really hard foul that could be a red, another for a soft tackle."
Meanwhile, Gracia wants to see improvements in Holebas' discipline next season and says, while the club accept his yellow card record, something has to change.
"Jose, it is true, this season had a lot of yellow cards. I think he has to do better for the next season," he said.
"In my opinion there are different yellow cards and some of them you have to improve in your behaviour.
"I try to speak with my players about all these different yellow cards and if it is something you can avoid you have to do it.
"I'm sure Jose knows it, all of them know, they have to try and improve something. In this case, everyone knows Jose and at the end of the season he always has a big amount of yellow cards.
"It is something we have to accept but not accept without doing anything – you have to try and improve."