The ELF file is actually only in design sources, it is not added to the simulation sources.
However, due to an incorrect flag (USED_IN_SIMULATION), the file shows up under the simulation hierarchy.
This will not cause incorrect functionality, this is a visual issue only.
A user can set USED_IN_SIMULATION to FALSE for the ELF file in the design sources to remove the duplicate.
This issue should be fixed in release 2014.2.