When running two (or more) instances of abipkgdiff in parallel, the instances walk on either toes. This is because the temporary directory used by abipkgdiff to extract the packages is not unique. Note that this was initially filed downstream at https://bugzilla.redhat.com/show_bug.cgi?id=1315204.
This issue should be fixed in the master branch of the git repository by commit https://sourceware.org/git/gitweb.cgi?p=libabigail.git;a=commitdiff;h=326992f0e1c71b0fd20ffe4b31c901b5abcd604a. The fix should be available in the 1.0.rc3 release.