This is the way it works:
You have three tickets all same issue; #1, 2 and 3. You merge them into the newest ticket which is #3. 1 and 2 get closed and a note is added #3 for each of the other tickets. Now #3 contains references to #1 and #2 and remains open until a tech closes it.
There are some options in Setup for Merged Tickets behaviour so you might need to check here:
Setup> Tickets> Status Types> Options> When Tickets are Merged
You can even have it delete those duplicate tickets if you want. Ours go to Cancelled instead of Closed so I can easily exclude them from reports & such
That was it. My settings were "When Tickets are Merged" Set STatus of Child Tickets to "Open". I have now set them to "Closed". Thank you.