refineMesh creating ugly cells at refinement interface.
 

I'm trying to use refineMesh but it's creating these extra cells at the interface between the unrefined cells and the refined cells. The new nodes that are created by the refinement at the edge of the interface are being connected to existing nodes in the unrefined mesh. Does anyone know if something is causing this or if there is some option I can activate to stop it?

-> checkbox 'decompose polyhedra' in paraview

It looks good but will simpleFoam still solve through those cells?

did you try? -> yes

but these cells should not be at "the point of interest"

Unchecking decompose Polyhedra will not change your mesh, its merely a visualization thing in ParaView. The best measure of whether your mesh will run is using the checkMesh utility by running

and seeing if it fails the mesh checks. If it does then you will have some problems. Good luck.