They have had very bad start in this season but I believe that they will recover from this mini crisis and return to top positions later. Even without two early bad matches, Atletico Madrid in my opinion nearly can not compete for La Liga title with Barcelona and Real Madrid. These bad early matches make their race for a third or fourth position more difficult but I believe they will get it at the season ending.
Atletico Madrid needs to make changes to compete for third place by the end of the season, and letting the previous two matches play out will make it difficult for them to perform consistently.
Sometimes teams don't start the season smoothly, and they'll constantly try to fix any shortcomings, and that's often the case with Atletico Madrid.
While I'm confident they can reach the top three by the end of the season, the team's weaknesses need to be addressed immediately by the coach, because if it continues it will make it difficult for them to catch up to the big three position..