The Pipeline Phase field on the Opportunity is auto generated with a prefix number that represents the then current sort order of the Stage Category's global option set. When the order of the options is changed, the existing Opportunities are not updated to reflect the current sort order.

This causes problems when creating a chart that uses this field as the unique set of values might include something like 5-Identify and 8-Identify that causes opportunities that are in the Identify phase to be split among the two options in this example.

Please consider using only the current phase's label without the numeric prefix, or provide another mechanism (such as a calculated field) to ensure that all existing opportunities reflect the new prefixes.