I think this might be related to how we put a pre-generated worker package in the workflow directory. Then we have a staging jobs which tries to do the same again:

kinc-1475173297/00/02$ cat stage_worker_local_kinc_0_local.out
2016-09-29 13:21:48,171 INFO: Starting transfers - attempt 1
2016-09-29 13:21:50,173 WARNING: cp: src (/local-scratch/rynge/workflows/kinc-1475173297/workflow/kinc-1475173297/pegasus-worker-4.7.0dev-x86_64_rhel_6.tar.gz) and dst (//local-scratch/rynge/workflows/kinc-1475173297/workflow/kinc-1475173297/pegasus-worker-4.7.0dev-x86_64_rhel_6.tar.gz) already exists and are the same file