You probably have, by all possible means, 7 noded blocks in HEXA. The unstruct hex mesh writer in HEXA cannot handle the corner where you have 7 noded elements sitting. So, when it writes the mesh, it does not write these elements in the mesh.
This gives hole in the mesh, resulting in missing faces and uncovered faces etc.. BTW: You might also get some bad determinants reporting for those corner elements inside HEXA while they may actually look good. Hexa, MED and at times most of the unstructured solvers cannot handle the 7 noded elements. There is a work-around to deal with this: • You should write a multi-block mesh from HEXA.
If you have too many blocks, you can first mesh the topology, then switch on "Output blocks" from the right side Display panel and then say "Blocking > Init output blocks" to initialize the output number of blocks. At this stage, whatever you work on will be saved only in the output blocks and not in the actual topology. You should then do "Blocking > Merge > ... more.
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