Description
The diagram rule you are trying to configure on your template can add diagram features that may already exist in the diagram as aggregated features; that is, as reduced or collapsed features.
Starting at ArcGIS Pro 2.4 and ArcGIS Enterprise 10.9, rules that add features, such as the Expand Container rule, Trace rule, and Spatial Query rule, must be configured before diagram rules that aggregate features, for example, Reduce Junction, Reduce Edge, and Collapse Container.
Solution
Change the current diagram rule sequence on the diagram template so rules that add elements come before rules that reduce or collapse them.