As with most things in TFS you get more than you bargained for. In this case I am seeing more file changes during the merge than I was expecting.
I have 2 child bran
If you need to merge a specific changeset you need to use the following statement:
tf merge /baseless /recursive /version:C95654~C95654 branch2 branch1
(It means ONLY changeset C95654).
The commandline you are using means every changeset before and with C95654.