The simplest explanation is that the one reference contains more assembled sequence (i.e., is larger) than the other, so the coordinate does not exist in the smaller reference. Similarly, a larger interval of multiple coordinates can collapse into a single coordinate in the smaller reference (or repetitive regions in the larger one may have been represented only once in the smaller assembly).

Thanks for your answer. As I read it I realize my question was not detailed enough. As the reason you have explained for the case where multiple coordinates may collapse, I meant to ask about biological reasons that may explain the discrepancies mentioned in my question. Thanks!