XDCR not replicating all documents, but no errors

I have one way XDCR setup between to replicate three buckets from a Couchbase Enterprise 3.0.1 server to a Couchbase Community 4.1.1 server. The third bucket had about 682747 docs on the source server when replication finished, and only 682682 documents on the target server. There are no errors shown on the XDCR page in the couchbase admin console, or the logs page on the couchbase admin console of either servers, or in the xdcr.log file on the source server. We do not have TTL setup for any documents. We are using sync gateway on the source server though. Is there any reason why some documents would silently fail to replicate and aside from comparing the entire keyset on both servers is there a way to find out which documents failed?

UPDATE: After about 30 minutes the number of keys matched. Any reason why 99% of the keys would get replicated in less than 5 minutes, but the last few dozen would take 30 minutes? Note, this is not a very active server so there aren’t many documents coming in.