CarpetRegrid2 supports both RotatingSymmetry90 and cell-centring. I do not know whether this case was tested, but even if so, there may not be a test case which means it may have broken at some point.
I don't know why "assert (all (iaxis0 % istr == 0))" fails. This may be because cell-centring is not supported, or because this routine makes an assumption about how Carpet lays out grid cells with respect to the finest grid, or because of an error in the parameter file.
Could you open a ticket, and attach the parameter file as well as some debug output, i.e. the values of reflevel, bb, bnd, axis, iaxis0, hh.baseextent(0,rl)?
-erik