Hi @NicoHV!
This is working as expected as far as I can see. I’m afraid the problem is that you’re trying to do this all with a single action and that will not always be possible. It may be necessary to divide and conquer 
To start, please familiarize yourself with the following 3 features. All can do similar things with limitations. One may be more suitable for a given situation
- Micropoly :
https://help.maxon.net/zbr/en-us/Content/html/user-guide/3d-modeling/modeling-basics/dynamic-subdivision/micropoly/micropoly.html
- Nanomesh:
https://help.maxon.net/zbr/en-us/#html/reference-guide/tool/polymesh/nanomesh/nanomesh.html?Highlight=nanomesh
- Micro Mesh:
https://help.maxon.net/zbr/en-us/#html/user-guide/3d-modeling/micromesh/micromesh.html?Highlight=micromesh
Please note that all of these are completely dependent on the underlying mesh topology. If it is not aligned or poorly shaped, your results will be also. When working with the small scale of cloth-like fiber detail this is not easily seen. However if you are using the feature to create large pieces of geometry, any alignment issues will be very clear to the naked eye.
Of these, Nanomesh is the most complicated but also the most powerful. It may offer superior control in some situations. However, since you asked about Micropoly:
The problem here is that the underlying geometry is too complicated to align in a single step. All the tunnels and holes create complicated edge alignment. Note that in the documentation, this feature is intended to create cloth style meshes on square 2d grids with uniform polygons.
However, you can get much better results working section by section. Your primary tools for aligning the polygons will be
-
Tool> Geometry> Dynamic Subdivision> Micropoly section> “Align”, “Rot Z” and “Rot X”.
-
Tool> Geometry> Modify Topology> Spin Edge and Align Edge
Please note in the following image I have selected the shirt of the DemoSoldier file that comes with ZBrush. I have deleted subdivision levels and switched on Dynamic Subdivision with Micropoly on, and no additional smoothing. No matter what I do, I will never get all the polygons to align their edges with a single operation. Changing the alignment of one changes all others as well.
Instead, I need to first isolate the problem polygon groups one by one, and align them individually. If you are not familiar with the shortcuts for working with mesh and polygroup visibility in the program, I encourage you to commit these to muscle memory. Masking will not be sufficient here. Working in the program is much more difficult if one is not familiar with how to isolate polygons:
https://help.maxon.net/zbr/en-us/#html/user-guide/3d-modeling/modeling-basics/mesh-visibility/mesh-visibility.html?Highlight=mesh%20visibility
You’ll notice on the front of the shirt there is a group of two polygons that simply will never match the others. So I toggle Dynamic SuBD back off and hide everything but that group. Im using ZModeler to quickly assign unique poly groups to problem polygons to make them easier to hide/unhide at will.
Once I have that group isolated, a quick tweak with Modify Toplogy> Spin edge should spin the edge for only those polygons, allowing them to fit with the rest:
From here simply go area by area, and adjust problem spots individually. Switch Dynamic SubD back on to check your work.
However, nothing can be done about the shape of those stretched polygons. This will influence results. For the best results, you want completely uniform, square polygons, but this will seldom be possible for complicated garments. In some cases you may have to manually reshape the polygons in an area, create the mesh section by section, then weld the points on the mesh sections after the fact. You may also need to manually insert pieces of geometry to stitch together sections of uniform mesh. This is easier to do with Nanomesh.
Hope this helps!
