It's very first months of Xabi Alonso in Real Madrid and he still needs to have more time for his management and tactical training for his players. So far in general, I think Xabi Alonso has done his management well in Madrid and 1 point difference with Barcelona is not too big. However, losing big in the Madrid derby is bad and he must improve his player mentality in big matches as in the last season, they lost in all direct matches with Barcelona, lost big.
Yeh Alonso need just more time, he just only spent a month and a half around with real madrid. Currently he is trying to experimenting with different tactics and therefore he is performing slightly not best. In m opinion losing one match isn't a big deal but several other can make it worse. Anyway the reason behind recent atletico defeat were lack of thier main players as few of the key players such as Rudiger, Arnold, Mendy weren't available, and due to that absence team's defensive approach were very weak and conceded a big lead. Anyhow now we have to think about the next matches which are with Villarreal. Villarreal were performing well currently while Real madrid will need strong enough efforts otherwise due to point drop real madrid can fall further behind in the competition race.