I have experienced this as well.
I try to merge compositions and sometimes it simply does not work. In all the cases that have happened to me, it has been that one of the pairs was already a merged composition.
I have found a workaround for the few cases where this has come up. I go to Settings / Library / Un-Merge Compositions and select the composition and un-merge it. Then I can go back and select all the occurrences and merge them, and it has worked fine. Hope this helps. Would be curious if it works for you.