basically I keep hearing people talking about keys and such do I need one or something?

I got the humble indie bundle version of the game and feel as if it might be missing something

No, Build 24, the Humble Indie Bundle version is DRM Free, the liscensing system was removed from it to comply with the rules of HIB, Build 25 will most likely need a key, but Data will find a way to incormporate HIB buyers into it.

I've had the same problem. I have it from the indie bundle and we get no activation key. But as far as I can tell the game doesn't update independently. I downloaded the limited version from the site and it has been majorly updated with tons of cool features. So basically if we want these we have to buy it again.
Is that how it is?

The HIB version is the latest version, the site has the previous version uploaded to it.
If you want the older builds, yes you would have to purchase a key, but I don't see a reason why you would want it.