Hi,
We had the same issue, and in my opinion it is caused by the parallelisation of sapcar during SUM phase PREP_PRE_CHECK/SCANDIR_EPS0
I did see several parallel SAPCAR jobs running during this phase.
So what happens when one job extracts SIGNATURE.SMF at the same time another job tries to finalize its extraction by setting the permissions for /usr/sap/trans/EPS/in/SIGNATURE.SMF?
It can happen that permissions are being set at the same time another sapcar yust deletes this file to begin extracting.
Since we had 146 SAR archives that needed to be extracted, a retry allways ended up in 4 to 12 conflicts.
What did do the trick was adding
/sapcar/extrcact_parallel = 0
to the file
../SUM/abap/bin/SAPup.par
Just as Christoph Langer suggested.
We had to restart the whole phase, a repeat was not enough to solve the problem.