Emery's men dropped to fifth in La Liga after suffering their second straight loss and third in four league matches, with Valencia replacing Sevilla in fourth after a 2-1 victory at Espanyol.
Pedro Leon's 85th-minute goal secured the three points for Getafe in Madrid and Emery seemed to admit he had overworked his core starting group.
Emery has started 20 different players across Sevilla's 11 games in all competitions since Spanish football resumed in 2015.
At Getafe, Sevilla lost midfielder Stephane M'Bia in the 16th minute to a sore hamstring, while Iago Aspas was subbed off with 34 minutes remaining after complaining about a thigh problem.
"We lacked intensity and we lacked clarity," the 43-year-old coach said, according to AS.
"The team was competitive though but we just lacked that extra ambition at certain moments and our finishing wasn't up to scratch - especially from the balls we played in from either wing. We suffered most going through the middle because Getafe would just steal the ball from us.
"Maybe now is [a] good moment to start recovering players and give some of the rest of the lads a breather. We have a few players who are low on fuel, they need a break.
"But the overall sensations are still positive; if we keep a cool head then we will put ourselves in a good position in the table."
Sevilla's next match is against Cordoba on Saturday.
It will be their first week in six without a mid-week fixture.
