Sorry, I was unclear. I'm referring to a situation in which the upstream build starts more than one of the same downstream build, all of which are linked by fingerprinting. From my understanding, you're referring to a situation in which the upstream only starts one downstream build (of which more than one have been triggered in the past).
For example, imagine a situation in which you have one upstream build. It's purpose is to run tests in parallel. To do this, it just runs 2 downstream builds that each run half of the test suite. All of these are linked by fingerprinting on, say, the upstream's BUILD_TAG. The bug I'm reporting it that attempting to copy artifacts inside upstream for "downstream build of (upstream, $BUILD_NUMBER)", artifacts are only copied from the downstream build with the highest build number. In this situation, I'd expect artifacts to be copied from all downstream builds.
Let me know if you need more detailed reproduction instructions – I can get them to you tomorrow.