I'm using OS X 10.11.2 and I have two external drives (USB) that I've erased (HFS+ Journaled). I upgraded from Yosemite. When I try to create a back up, my MacBook Pro Retina is stuck in the Calculating stage. On both drives. Erased both drive twice.
Did you exclude the Time Machine drives from Spotlight indexing?
Only yesterday, I created a new Time Machine back-up on a reformatted HFS+ disk, so it isn't El Capi.
Unless something went wrong when installing it. In your case, it's highly unlikely that two drives failed. And I did exclude the disk from Spotlight indexing (a lengthy process).