Are these notification highlighted in the menu with a different background color (i.e. unread)? If so, this is expected after enabling the new notification menu for the first time because in the new notification menu, unread notifications are prioritized which means they’re shown first no matter how old they’re. Once they’re read or dismissed, they should revert back to their old position in the notifications menu. However, as Jammy said, this doesn’t sound right:
After dismissing, do the old notifications remain highlighted in the menu? Or have they lost their highlight but are still stuck at the top? Does this persist even after a full page reload? Are there any errors in the console after the user clicks the dismiss button?