On servers with bursts of data changes the system table space tends to grow due to UNDO segments stored there and cannot be shrinked again. The current workaround is to take a logical backup, reinitialize the data directory with previously configuring separate UNDO tablespaces and reload the data from the mysqldump file. For large databases it should be possible to move UNDO segments out of the system table space without rebuilding the whole data directory. This process is unacceptable due the long downtimes caused by exporting and re-importing the data.
In new installations UNDO tablespaces should be default.