To anyone having the issue of a reuseable element showing as duplicated in the editor here is how to resolve it.
Put all elements within the reuseable element within a group.
I had reached out to bubble support to debug this and they told me it was just my browser. I didn’t accept that since it was only some reuseable elements that had the issue - so it must have been something those elements did different than the others. The issue was that they had elements not within a group.