I had a run time error when using flann::AutotunedIndex for a small set of 2d points (like 10-20 points). Possible solution is not to use flann::AutotunedIndex for such low dimensional data as mentioned here and here.
The cause might be flann::AutotunedIndex cannot reach high enough precision at buildIndex. In such cases, better to use exact kd-tree (flann::KDTreeSingleIndex).
