In PhysiCell_standard_models.cpp's standard_volume_update_function I believe the calcified fraction update is not correct. All dynamic volumes except it are updated following a forward Euler method, e.g.
phenotype.volume.fluid += dt * phenotype.volume.fluid_change_rate * ( phenotype.volume.target_fluid_fraction * phenotype.volume.total - phenotype.volume.fluid );
The calcified fraction update does not have the + in the +=. It reads
phenotype.volume.calcified_fraction = dt * phenotype.volume.calcification_rate * (1- phenotype.volume.calcified_fraction);
This means the cell will never calcify completely, it's calcified fraction will fluctuate around dt * phenotype.volume.calcification_rate