Select by Attributes is not supported for 1:M joins when there are duplicate OBJECTIDs in the attribute table. The selection doesn’t work as expected; incorrect rows are selected.
Select By Attributes on joined data — For rows that are 1:M, all rows in the join table get selected...
That limitation is currently unfixable. Instead of confusing users with wrong selection results, I’m wondering if it would be safer to disable Select By Attributes in this specific scenario — when the Duplicates warning is present in the attribute table.