We deploy IE 10 via SCCM 2007 and had the same issue so hopefully its the same for IE 11. The problem is caused by IE setup only allowing 10 seconds for the WMI query to finish, but WMI could take up 20 seconds to complete so it fails on a random number of machines. The next step taken by IE is to get the patch from the Internet and if your like most businesses the computer system account won't have proxy access to get out so the installation fails.
The fix or I should say workaround is to run the following script before the installation, which will then cache the result and will typically allow the IE install to complete as the query will for us anyway respond in about 5 seconds. We depoly this script about 5 minutes before the maintenance window for patch installation which opens at 11:00PM which gives us much better success.
So if your a deploy unattended another way or manually just run the script before installation.
Hope that helps
On Error Resume Next
strComputer = "."
SET objWMIService = GETOBJECT("winmgmts:\\" & strComputer & "\root\cimv2")
SET colItems = objWMIService.ExecQuery("Select HotFixID from Win32_QuickFixEngineering where HotFixID='KB2729094'")
FOR EACH objItem in colItems