Despite their ragged form, Real are joint top of the La Liga table with Barcelona and Alaves, although Barca will march three points clear at the top if they win at Valencia on Sunday. "Today we had some good chances but the injuries to Bale and Benzema punished us a lot", he added.
Alaves, whose fortunes have been transformed since coach Abelardo Fernandez took over last December when they were fighting against relegation, rose to a third.
Lopetegui was forced to take early action in the second half due to an injury to Karim Benzema, bringing on centre forward Mariano Diaz which briefly led to Real playing a more direct game.
Alaves continued to snaffle out any danger, though, and when the deadlock was finally broken it was down the other end off the head of Garcia, who turned the visitors' frustrations into despair.
"Karim and Gareth had injuries, so we had to make decisions regarding changes", he said. I think we started the game quite well, which is what we wanted, but the fact we have not scored has punished us.
Real Madrid don't usually welcome the worldwide break, as there is always a fear of players picking up injuries while representing their countries, but the October stoppage is a timely one.
Similarly to the first half, the European champions were finding it tough to carve out clear-cut chances, while they looked out of ideas without Isco and Marco Asensio, who surprisingly benched.
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