The following Internal Exception has been seen intermittently in Vivado Hardware Manager when loading, importing and viewing ILA data files:
This issue has been observed with multiple projects and is not specific to a particular device or device family.
The error occurs when loading or refreshing the ILA data file for a generated bit file.
The issue is seen only on Windows operating systems and is due to a low level Java directory call returning the C:\.Xilinx directory instead of the C:\Xilinx directory in certain cases.
To work around the issue, remove or rename the "C:\.Xilinx" directory. In many cases, the "C:\.Xilinx" directory contains license files that are needed for Vivado, or the operation of other Xilinx software.
In this situation, you should copy the license files to another directory (for example, C:\Xilinx_lic) and point to the directory with the XILINXD_LICENSE_FILE environment variable.
A fix for this issue is scheduled for Vivado 2016.4.
See also (Xilinx Answer 67499)