Following workaround might not be feasible in all instances ,especially if you are pushing the updates through SCCM or other software delivery/deployment tools.
Reason for the error is one of the .MSP file which included in the .exe file is Hotfix 3 for AutoCAD 2016. This can’t be installed on AutoCAD 2016 Sp1.
If you extract .MSP files from the exe with the following command line, you will find 2 .MSP files.
Map3D2016_x64_Sp1.exe /e Map3D2016_x64_Sp1.MSP
Only second file needs to be applied to Map 3D 2016.
Msiexec /p Map3D2016_x64_Sp1.MSP /q
Note:/q is important for the above command line, else you might get following error.
Similar workaround might be required for Civil 3D 2016 Service pack 1 as well.