The system is probably confused by what it's reading from the reservation. While the receipt and tickets show correctly, the reservation still has the original flights listed in it, albeit they now are marked as canceled, nothing ever is deleted. The system is seeing that segment (which would be right before the new flights are listed) and is accidentally showing it online.

It's just an issue with how the information is being interpreted. As long as receipt and tickets show correctly, you should have no problems. Have had it happen with UA and other airlines.