Message limit doesn't mean just things you type, but any 'messages' to the server from your account.
If you're lagging and keep pressing buttons (instructions to the server from your account like 'hey move my character' or 'craft this thing') when the lag passes they hit the server all at once and think you're spamming commands.
Also happens if you're researching a lot of alchemy recipes very quickly, the server doesn't know quite what to make of it and boots you.
It could also be caused by addons trying certain things, but you're not using addons.
When you're lagging and nothing's happening, just sit tight and don't give any input more than once.