I've encountered this, too, and I can confirm that it's neither an X-Keys or a KeyClone problem. WoW just likes to be "helpful" with keybinding matching sometimes.

I found two solutions. Before I really delved into the wonderful world of add-ons, I just got into the habit of "unbinding" most of the standard action bar keybindings on a new character (since I found that I ran into this most often when using Alt plus some number 1 - 10). Now, I've become devoted to macaroon for my bars and macros, so I just remove the icons from the Blizzard action bar before I uncheck the "enable Blizzard interface" option in macaroon and start building my own bars. While I have not done really extensive testing, I've not run into this type of problem with my macaroon keybindings.

Hope that helps!