https://bugs.launchpad.net/percona-server/+bug/1656022
TokuDB uses PerconaFT get_fragmentation function to calculate free space in data files. This is a bad choice as this function walks the entire PerconaFT dictionary block table to tabulate up all of the free space within the holes. This is entirely unnecessary and can cause application stalls for use cases with huge numbers of nodes.
Along these lines, TokuDB also only reports actual basement node sizes and not internal nodes/messages in the 'data' size.
See also.