Madrid's 3-0 first-leg win meant Wednesday's 1-0 defeat at Butarque was not enough to send them out of the tournament at the expense of Leganes for the second year in a row.
Solari gave Isco a start in a rejigged team that saw Marcelo feature on the wing in the first half, with Madrid struggling to create chances without a focal point in attack.
And Solari accepted his side, who have lost two of their last four matches, were not good enough against Leganes, who won the second leg thanks to a first-half Martin Braithwaite goal.
"A weak performance, above all the first half," he told a news conference.
"They all needed to get playing time, they got it. We got through the tie, but the performance was weak.
"Sometimes we try things and if they do not work, we try to improve them.
"We have lacked depth. We paid not having a specific reference in attack."
Madrid were without Karim Benzema, the striker having fractured his finger in their 2-1 win at Real Betis in the league last time out.
"It is a broken little finger," he said of the striker. "We hope to have him at the weekend, and next Wednesday, and the next weekend."
Isco lasted 68 minutes on a rare start under Solari, with the playmaker withdrawn for Cristo Gonzalez.
The Spain midfielder completed 93 per cent of his passes but wasted Madrid's best chance to score with a tame shot.
Solari has regularly been questioned about his apparent lack of faith in Isco but he once again dismissed talk of a rift with the playmaker.
"There is no problem, not at all," Solari said of Isco.