I see error in pgbouncer saying 'server conn crashed'. Could it be possible that because I set idle_session_timeout to 30min.
Seems like a reasonable scenario.
Also application team getting an error, duplicate values violate constraint's. Is this error possible because of pgbouncer lag ? Or sequences or pure application side issue?
This requires actually debugging your system, not generalities. But 'pgbouncer lag' doesn't really seem like a thing. Concurrency timing issues are a thing to be aware of though.