A funnel report requires the object move through the stages in a sequential order. However, if a stage is accidentally skipped or a new stage is added in the middle or the pipeline, the report no longer calculates the data correctly because (from what support has told me) it uses the initial stage flow in the calculations.
Ideally the report could account for the ‘stage has ever been in’ scenario so even if a stage wasn’t hit sequentially it would still get included.