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The user is added to the site but unable to see the term, but is able see the page by typing URL manually.
While searching I could not find much except this post that didn't tell me much. What work around are their for this issue?
I know if you give them contributor permissions they are able to see it. This is not ideal, because it means they see other things they aren't suppose to.
When working with Managed Navigation, menu items linked to pages with specific permissions set are automatically hidden from users without those permissions.
When using the Managed Navigation and modeling the site navigation with Terms, as long as the particular Navigation Term is linked to a page using the Term-Drive Page with Friendly URL option, the term will be displayed to users only if they have the necessary permissions to access the associated page.
Sorry for the confusion. Any workaround if it works will be a good answer for me or someone with the same problem. Just making it easier for other people in the future looking for this problem