I just committed a change "CarpetRegrid2: Try harder to combine different refined regions". This may affect the grid structure you see during time evolution.
When a refinement level consists of several regions, then CarpetRegrid2 tries to combine these into a single, cuboid region, adding additional refined points in the process. Having fewer regions with a more regular shape helps efficiency. CarpetRegrid2 then checks how many new refined points needed to be added in the process. If this number is small, the single region is kept; if this number is too large, the single region is discarded, and the original set of regions is used instead. The parameter "CarpetRegrid2::min_fraction" determines this, and setting min_fraction=1.0 disables this grid structure optimisation.
This change slightly modifies this algorithm in CarpetRegrid2, and may thus lead to a different grid structure.
-erik