Artur Boruc kept out Holt's subsequent spot-kick, but Southampton players continued to protest after the final whistle in the 0-0 draw and were joined on the pitch by manager Mauricio Pochettino.
The club have until 4pm on Friday to respond to the charge.
"If people cross the line, then of course you have to be charged, but I think at that moment we were fighting to keep that clean sheet," Hooiveld said.
"We had fought the whole of what was a tough game and tough circumstances, then they were awarded a penalty which in our eyes was not the right decision.
"Then the emotions went a little bit high and maybe we got a little too close. I think whatever happens after that, it is not up to us to decide."