Barca needed a late goal from substitute Ivan Rakitic to see off a determined Athletic side and although they picked up a third win in four matches since the season re-started, they again failed to sparkle.
"When teams offer you little space you have to be very precise and agile and we have been lacking that since we returned," Setien told a virtual news conference.
"It's not been easy and we are missing something overall, a bit of spark. Our opponents have a lot to do with this because they are sticking together and leaving hardly any space and we're finding it hard to open them up.
"But I think we'll start to find it easier the more the season goes on."
Barca thrashed Real Mallorca 4-0 on their return after the long break but looked rusty in last week's 2-0 victory over struggling Leganes and on Friday were held 0-0 at Sevilla, allowing Real Madrid to go top of the league on Sunday.
The win over Athletic took Barca three points ahead of Madrid but Zinedine Zidane's side will go back to the top of the table with victory over Real Mallorca on Wednesday.
Setien was not pleased with how his side started against Athletic but praised youngsters Riqui Puig and Ansu Fati for helping to open their opponents up when they came off the bench.
"We were more relaxed in the second half and played much better. Ansu and Riqui gave us dynamism and allowed us to have longer periods of possession," Setien said.
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