Chatter email notifications direct user to Experience Site

1. The notification's recipient is a part of the site where they're set to receive notifications but are not set to receive chatter notifications internally.​ The application checks to see if Chatter Email notification preferences are set internally first and then for each site for which the user is a member. It's recommended to set the same Chatter Email Settings or preferences both internally and within each site where you're a member.
2. The affected user's assigned profile has been assigned a default site. All emails sent, whether for internal chatter mentions or not, would be branded for the default site. See Assign a Default Experience to a User Profile or more details.
3. You have two active sessions in your browser:

Window/tab 1: You are logged in to your main internal org. 

Window/tab 2: In a separate window but the same browser, you subsequently logged in to your site. 

 

When another user replies to your comment, the link will direct to site login. 

To address this, make sure to use different browsers to login to internal org and site. This way the browser won't apply your last login and assume that you are still in site. User should also ensure that they enable notification for internal chatter posts as well.