I haven't tried pushing IE11 out yet, but when we rolled out IE9 we created a new repair task just for that rather than include it in our monthly patch cycle. It installed without issue.
Can you check to see if your "IE11" definition is set to "Scan" in Patch and Compliance and downloaded to your core server?
You could also download it from Microsoft and create a package for it. You would need to check it's command line options to see if there is anything about the installation you want to change (I always go for silent + no reboot options when I can).