The issue of FA values greater than 1 is basically due to noise, and the fact that the tensor fitting process in MRtrix3 is unconstrained – as outlined in this post and this post. Using multi-shell data in the tensor fit can also contribute here, since the DW signal does not decay mono-exponential (which the tensor model implicitly assumes).
Also, check which voxels have FA>1, you might find they’re predominantly non-brain voxels…?