You need to choose 1 or more packages from your target and destination schemas and share them here with the expected and acutal results so we can reproduce the problem locally. If you don't want to share the code publicly, then open an SR with MOS.
Maybe this is the following case:
"Package bodies (DDL) on both source and destination database are identical but package body on the source database is marked as "invalid" and package body on destination database is marked as "valid" - then Database Diff reports that package bodies different. (but on panel showing DDL for both compared package bodies there is visible no difference)."