When you create a feed which requires multiple cycles, a duplicate entry is produced. This is due to bug in the LIMIT part of the query.
On cycle 1 the limit is 0, 1000
On cycle 2 the limit is 1000, 1000
So the product in result position 1000 is brought in during both cycles.
A workaround for this issue is to increase the amount of items per run. If you bump it up to 10,000 instead of 1000, you can avoid the issue altogether if you have less than 10,000 products.