I have had several instances this happening when I am pulling in a layer from portal or AGOL into my map through the catalog in Pro 2.5 and 2.6. If I set a definition query in the layer properties in the Pro map, geoprocessing tools do not seem to honor it. First time this happened I performed a field calculation on 50 records queried out but it ended up running on all 6,000 records. Is there an environment setting I am missing or has anyone else seen this behavior?