The Blues needed a late equaliser from Fernando Torres to avoid a huge shock, with the Bees ahead twice at Griffin Park.
The holders are unable to host the replay until fifth-round weekend.
"Yes, it's quite difficult for us," Benitez said.
"We play one game every three days so, if you understand, how can you train the day after? How can you train the day before games when you have the same players all the time?"
Benitez appeared more downbeat than at any stage since taking charge, amid reports the club were reluctant to back him in the transfer window.
The Spaniard nevertheless branded Chelsea's first-half display as unacceptable.
"We made too many mistakes in the way we wanted to play," he said before hailing their second-half "character".
Benitez insisted Chelsea were denied a "clear" penalty and once again defended his team selection and tactics amid renewed chants of "you don't know what you're doing" from supporters.
"I can guarantee that playing Juan Mata, changing the game, we know what we are doing," he said, revealing he decided to pick Ross Turnbull in goal after Petr Cech picked up a knock.
- Sports & Recreation