If you run a command script that includes IOS CLI filters and deselect the checkbox to "show commands in output", it incorrectly displays the part of the command after the CLI filter anyway.
Example: my script is "show ntp assoc | e address|synced". Wtih "show commands in output" deselected, it still logs the "|e address|synced" to the output file.
On the feature side, it would also be really nice to be able to log all the output to a single file instead of one file per node, so I don't have to concatenate the output with post-run text processing tools.