stage in jobs repeat portions of deep LFN's

for some of the LIGO workflows we are seeing stages jobs repeat parts of deep LFN's, resulting in the jobs failing.

For example for LFN - 113523/L-L1_HOFT_C02-1135235072-4096.gwf

 dags/work/main_ID0000001.000/00/00/stage_in_remote_local_0_0.in
[
 { "type": "transfer",
   "id": 1,
   "src_urls": [
     { "site_label": "local", "url": "file:///cvmfs/oasis.opensciencegrid.org/ligo/frames/O1/L1_HOFT_C02/L/1135/L-L1_HOFT_C02-1135235072-4096.gwf", "priority": 100 }
   ],
   "dest_urls": [
     { "site_label": "local", "url": "symlink:///home/steven.reyes/projects/cbc/ER10/pycbc-v1.5.4-verification-workflows/pycbc-masterSettings/output/local-site-scratch/work/././main_ID0000001/00/00/113523/113523/L-L1_HOFT_C
02-1135235072-4096.gwf" }
   ] }
]