The optimizer can perform a variety of optimizations on an aggregation pipeline.  These include reordering of stages as well as coalescence.  Such modifications allow the database to improve the performance of the pipeline.  

To determine if any of these optimizations have happened, a user must be aware of their existence and then compare the stages output from explain with the original pipeline that was submitted.  Explain could help facilitate this process more directly by indicating specific optimizations that were performed.  This could be done via simple boolean flags or could be more complex and list out the transformations individually.