Hi aneeshakasim,
Thanks for using Apple Support Communities. It sounds like you’re having trouble with WhatsApp messages coming late. I’m happy to help.
To start, I suggest making sure you have Background App Refresh enabled for the app. You can do so by tapping Settings > General > Background App Refresh.
While the title of this app may not seem to pertain to your issue specifically, they’re good steps to try next:
If an app unexpectedly quits, stops responding, or won’t open - Apple Support
Should the issue persist, you’ll want to contact the app developer.
Take care.