I have notice that pwnfilter works but can not run and commands like comment, kick, ban, etc. Not sure if it's the filter or me I also noticed the cap filter is not changing to lower case, rest of filter filters swears, replaces or removes. just won't punish players

Yea this is one of the biggest bug/issue not updated.
Can you paste here a full config and filters here maybe using pastebin? by me work when i know from the last time.

PwnFilter development has stalled for quite some time, it looks like since the last release some changes have been made to bukkit/spigot that are starting to break this plugin. Unfortunately, there are no plans at this time to update for the latest versions of Minecraft.