There appears to be a bug with OS X 10.11 and 10.11.1, where Time Machine will stop backing up if you have a USB UPS attached. This has been reported to affect multiple UPS brands, including APC, Belkin, and MGE. Rumor has it that this has been fixed in the forthcoming OS X 10.11.2 update. The current workaround is to either unplug the UPS, or manually select the “Back up Now” option from the Time Machine menu on a regular basis.