To narrow down the error I cut the big RVE down to just one fibre (and the matrix surrounding it). It still did not work. When I model the same exact geometry "by hand" it works just fine.
The big RVE was created using a Ironpython script, so this must be source of the problem. Since it is a different issue (and probably not the meshings algorithms fault) I will start a new thread (https://forum.ansys.com/discussion/27993/sketch-created-by-python-script-causes-meshing-to-fail/p1?new=1)