InnoDB: "Only one log file found" after binary import
Assuming you have run innobackupex --apply-log successfully you either have a configuration problem (probably innodb_log_files_in_group is 1 in the original and 2 -or not set- in the restored server) or you lost ib_logfile1 somewhere in the process.

InnoDB is ok, it is normal for it to fail when it detects a different configuration on disk than on the file.

Please be aware that xtrabackup/innobackupex only copies data files, not the /etc/my.cnf.

Final answer: apply-log wasn't being executed successfully- a mistake while logging was concealing that. The actual error was due to a specific bug in an old version of Percona XtraBackup. Update to a newer version >= 2.1.8 should fix that.