Tables are shown different in Schema Compare when they have the same virtual columns pointing to their own schema's function:
CREATE TABLE tablename
(....
TOTAL_SAL NUMBER(10,2) GENERATED ALWAYS AS ("SCHEMA1"."FUNCTION1"("MONTHLY_SAL","BONUS")
CREATE TABLE tablename2
(....
TOTAL_SAL NUMBER(10,2) GENERATED ALWAYS AS ("SCHEMA2"."FUNCTION1"("MONTHLY_SAL","BONUS")
The functions are identical, the tables were declared identically, but in the parsing, Toad always adds the schema name and causes an inappropriate "Objects Which Differ/Columns" hit in the Results pane of Schema Compare.