java – Eclipse Debug mode doesn’t stop at the right break points

I am trying to run Eclipse in debug mode with Websphere app server. Websphere is configured for debug mode and eclipse configured for the same debug port under remote java applications. It is kicking in the debug mode but shows the debug/break points and navigation wrongly and any exception stack traces in server logs also shows the wrong line numbers compared to the java file in the IDE which confirms the same.

• Tried the usual refresh, clean all projects, build all, with no change.
• Checked that skip all break points is not selected. However, irrelevant as in my case it is stopping but showing the wrong lines.

Usually, it may happen when the compiler & runtime java versions are different for IDE vs App server. But my Eclipse .ini file, project’s(maven) build path and websphere points to the same JDK version which is 1.8. Yet, still facing the issue. What am I missing here ?