The total count will go up as the puller reads the incoming _changes feed from the server. It might then go down after the puller compares the revisions from the feed and ignores the ones that are already in the local database. So it might go up by 30 as it reads changes, then down by 18 when it turns out only 12 are new.
I’m wondering if you’ve got a loop somewhere, like something that’s indirectly responding to new revisions by making changes, creating new revisions. If you’ve only got 3000 docs in the server db, then the change count shouldn’t be going much over 3000 when pulling into an empty db.
The best thing to do is probably to run your app with ‘SyncVerbose’ logging enabled (http://docs.couchbase.com/couchbase-lite/cbl-ios/#enabling-logging), upload the logs to Gist or Pastebin or something, and submit an issue on Github with a link to the logs (https://github.com/couchbase/couchbase-lite-ios/issues).