Which version are you reindexing into exactly?
Can you share more details about how you create the index on the new cluster, and how you are reindexing data?
Something seems to be going wrong around routing of the documents. Elasticsearch doesn't enforce uniqueness of ids across different shards. The assumption is that whenever you index a document with same id, it will get routed to the same shard and replace the existing one, unless some custom routing is specified, or.... well let's why this happens to you.
Cheers
Luca