Now using correct ids as reference if we are informing about a new note.

app/mailers/emails/notes.rb

@@ -15,7 +15,7 @@ module Emails
       @issue = @note.noteable
       @project = @note.project
       @target_url = project_issue_url(@project, @issue, anchor: "note_#{@note.id}")
-      set_reference("issue_#{@issue.iid}")
+      set_reference("issue_#{@issue.id}")
       mail(from: sender(@note.author_id),
            to: recipient(recipient_id),
            subject: subject("#{@issue.title} (##{@issue.iid})"))
@@ -26,7 +26,7 @@ module Emails
       @merge_request = @note.noteable
       @project = @note.project
       @target_url = project_merge_request_url(@project, @merge_request, anchor: "note_#{@note.id}")
-      set_reference("merge_request_#{@merge_request.iid}")
+      set_reference("merge_request_#{@merge_request.id}")
       mail(from: sender(@note.author_id),
            to: recipient(recipient_id),
            subject: subject("#{@merge_request.title} (!#{@merge_request.iid})"))