"Index, Dimension 1, above upper bounds" type error

Hi Jeff, could you please help me figure out how to fix the tiny defects that can not be detected without zooming. I have tried different set of paras for cut-cell method but not obtain a perfect mesh. And @cgw also has helped to fix a bug with bug report I uploaded. Thank you.

https://mfix.netl.doe.gov/forum/t/how-to-eliminate-the-triangular-holes-defects-around-the-intersection-parts-from-the-generated-mesh/3250/6