This behavior is associated with something already reported as a bug: Receipts and Payments clone bug. There was another, related issue, as well, in which some clones duplicated all fields and other clones substituted the current date. That issue was resolved so behavior is consistent throughout the program. Unfortunately, the way it was resolved was to make clones be true clones in all respects, including reference numbers. As of now, the issue of clones ignoring the form default for automatic references remains. I agree it’s a problem. Hopefully, @lubos will resolve it soon.
For now, the thing to do is check the Automatic tick box for the reference when the clone appears, before clicking Create.