I'm seeing this same issue but only with enterprise geodatabases/sde connections. If I export the EGDB feature class to a File Geodatabase, the issue goes away. I'm using ArcGIS Pro 3.0.3.
Feeling like this is a bug, because the "Selection" filter appears when the Chart is first being created and is loading the data, but as soon as the data is loaded, the button disappears. Makes no sense for the Selection filter to disappear just because the layer is in an EGDB by design.