With the way things are going for them and how many games they are playing and how many players were on national team, it was estimated that Real Madrid would have been very very tired, which wasn't wrong and proven by the fact that they barely got the win here. If they keep this form going then they have a chance to win the league, but at the same time they need to figure out a way to rest some of their players too.
This is football and that's but an excuse, players go through very demanding training and conditioning session to prepare them for this sort of game time, beside they aren't the only team that had their players engaged with international duties. I think Leganes were just top of their game yesterday and really gave Madrid a run for their money.
Real Madrid is not an ordinary team an opponent team would just score and go free they must reunite and face the team and score it back to back unless the team is the among the top 4 teams in the league. Even Barcelona gap them with only 3 points and Real Madrid is in the second in the Laliga table. Well organized teams in any league come back in the second half to do well and for those teams that are not strong, come back with more weakness. Real Madrid is a strong team and can't be scored anyhow.