Temporary #sql files not removed automatically since update

I performed a maintenance update a few days ago and since then the disk usage grew considerable due to mysql temp files not being deleted.
Example from this morning:
-rw-rw---- 1 mysql mysql 3275751424 Oct 15 06:58 #sql-ib10877-701271144.ibd
Given the size this is related to
-rw-rw---- 1 mysql mysql 4366270464 Oct 15 09:44 live_positions.ibd
rm '€

Given the time at which this happens, it seems related to the daily database optimisation, dump and backup.
This occurs only since the update a few days ago (on debian 64b).
Installed packages are:
i A libperconaserverclient18.1 - Percona Server database client library
i percona-server-client-5.6 - Percona Server database client binaries
i percona-server-common-5.6 - Percona Server database common files (e.g.
i percona-server-server-5.6 - Percona Server database server binaries

Source: percona-server-5.6
Version: 5.6.15-rel63.0-519.wheezy
Replaces: libpercona-server-client18
Source: percona-server-5.6
Version: 5.6.21-69.0-675.wheezy

sources.list content:

deb http://repo.percona.com/apt wheezy main
deb-src http://repo.percona.com/apt wheezy main

All packages up to date on 14 Oct 2014

Did you run OPTIMIZE TABLE or ALTER TABLE on live_positions table, and did it fail? If live_positions is the only suspect, and if it is not likely to grow this table by 1G in 3 hours, then the size difference indicates that the data copy for the ALTER TABLE didn’t complete and so left over the #sql file. Please check the log from the daily job, error log from mysql for any restart, also check if there is sufficient disk space.