Never expected Croatia to lose against Turkey. But even now, there is no threat as such for Croatia. They are comfortably placed with 10 points and they are well ahead of Armenia and Wales. Armenia lost against Latvia as well, else they would have had the same points as Croatia. Also, let's not forget the fact that Croatia has played one match less when compared to both Turkey and Armenia. But the standings are not going to change anytime soon. Tukey's next match is against a weak Latvia, while Croatia will be facing Wales (who are in a state of suspended animation after the retirement of Gareth Bale).
I don't think anyone expected such a result in Croatia's match against Turkey. After all, the Croats seemed to be the favorites, they played at a new stadium, at home, the balance of goals scored and conceded was excellent, the largest in the group + 7 and such a sudden defeat. I would not say that Croatia is in no danger, they still have to play away in Wales, and usually at home Wales plays 100% and if they beat Croatia, they will be equal to Croatia on points.
In any case, Croatia have a good chance to qualify due to their matches against Armenia and Latvia, but now Croatia have made it harder for themselves to qualify. If Croatia wins, they would seem to be out of the group ahead of schedule.