Comment 1 for bug 1199555

--apply-logs-only is mandatory for archived logs applying because it is assumed that unfinished transactions can be finished during the further logs applying. Even if this option is not set by user explicitly it is set in xtrabackup.cc implicitly:

                /*
                  Unfinished transactions are not rolled back during log applying
                  as they can be finished at the firther files applyings.
                */
                srv_apply_log_only = TRUE;

The bug is reproduced without --apply-logs-only too.