I've been noticing this problem with increasing frequency. As I attempt to refresh a report, metrics do not update. However, if I manually drag in the same segment to a table, then the numbers will update. If I then remove the segment again the numbers return to how they were before. It seems as I drag segments in and out of table (the tables is a list of segments, not segments being applied as filters) the metrics change for no apparent reason. I will provide a screenshot of before and after for some context.
In this specific example, I've got a table with segments listed. I remove the one segment "Make Payment 2nd Page (New) - Hits" and the visits for each of the other segments change.