did 2k bundle run out of keys?

I can't answer your question, but you'd think they'd disallow sales and put up a banner if they ran out.

I think they imposed some limits on purchases, to fight resellers.
Try using a different method than your first purchase (like paying with card directly instead of Paypal).
Or just wait some time.

You can buy one bundle per payment method. It has been imposed on their bundles for quite some time now, started around the first Capcom bundle I think.

I purchased two bundles with same method. No issues.

^ Likewise. I heard they have a limit of three.

There is a bundle limit of 2 per account for this specific 2K bundle. Order will be declined thereafter. The developers have bound the site to this agreement to curb risk of resell of keys. You gotta love Indiagala Happy Hour and DIG BTA 2x bundles.