xindy(1) does various funny things if a filename contains characters
that are not usually used in filenames:

$ touch '>t0'
$ ls -l
total 0
-rw-rw-r-- 1 zefram zefram 0 Jul 17 01:21 '>t0'
$ xindy '>t0' 2>/dev/null
$ ls -l
total 0
-rw-rw-r-- 1 zefram zefram 0 Jul 17 01:21 '>t0'
-rw-rw-r-- 1 zefram zefram 0 Jul 17 01:21  t0
$ touch '|echo wibble'
$ xindy '|echo wibble' 2>/dev/null
wibble
$

These arise from its use of the <> Perl operator, which is not suitable
for the implementation of a read-from-list-of-files kind of command.
Because the range of misbehaviour includes writing to arbitrary files
and running arbitrary commands, this is a more severe bug than normal.