Dear dhruvilprajapati,
Good day! Thank you for posting in Microsoft Community. We are happy to help you.
May I know if you have SharePoint Server Publishing Infrastructure feature enabled under Site Collection Features in Site Settings?
Per my experience the sites which do not have this feature enabled, show three options i.e., Theme, Header and Navigation and site which has this feature enabled shows Theme and Header only.
Note: deactivating the feature will disable the features which depend on it and any user data or customizations associated with this feature might be lost. In this case, to change your navigation links, see Customize the navigation on your SharePoint site.
If the suggestion above doesn't work, may I know if the other sites have the same problem?
Sincerely,
Igor | Microsoft Community Moderator
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