Newcastle United suffered a third successive Premier League defeat yesterday.
Watford won 2-1 at thanks to goals from Roberto Pereyra and Andre Gray. Ayoze Perez was on target for Benitez's side.
Benitez had made two changes – Murphy and Javier Manquillo started ahead of Matt Ritchie and DeAndre Yedlin – at Vicarage Road.
Newcastle trailed 2-0 at the break after an error-strewn first half, and winger Murphy was withdrawn early in the second half shortly before Perez found the net.
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United went on to dominate the half, but they couldn't find an equaliser.
Asked about Murphy's substitution, manager Benitez said: "We cannot blame one player, because, I think, the team in the first half was very poor.
"We made too many mistakes. We cannot talk about 'this striker did not score, this winger did not do that'.
"We were poor as a team. In the second half, we were doing things in a different way. I changed the system, and we were a little better. For this system, Jacob was maybe not specifically ideal, so I took him off.
"But to change the system, I needed to do it."
Newcastle haven't taken a point since securing their top-flight status with a win over Arsenal last month.
"The team has been working so hard, that sometimes it's difficult to keep this level," said Benitez.
"We tend to change players – we tend to change things if we can – but we play against teams with quality too, and if you don't make the right decisions, then you can fall behind.
"These mistakes, and the experience that the other teams have, you pay for that."