One way this happens is if you have a script that has intercepted the /notice command using an alias of the same name, and does something different with it than it should. If you disable scripts with:
/remote off
and it stops happening, then the problem is caused somewhere in one of your scripts. Be sure to turn back on with:
/remote on
You can hunt for the offending alias with:
//echo -a x $isalias(notice).fname
If "/remote off" stopped it from happening, but there's no alias named notice causing this, there may be an event intercepting the INPUT event and using "msg" to display what you type in the editbox, even though they're supposed to treat input differently if they begin with /
If neither of these is happening, it's possible that you're at a new network that's causing it. The 'notice' command depends on the irc server to handle it correctly, and I wasn't aware of any irc servers not recognizing it until someone using Twitch said that 'notice' gave an invalid command error. It's possible for a server to handle incorrectly by sending it the same way as done by /msg