I have the same error. After changing option to show verbose output it shows:
An error occurred when merging assemblies: ILMerge.Merge: ERROR!!: Duplicate type 'DotNetNuke.UI.Skins.Controls.SolPartMenu' found in assembly 'App_Web_k5hhsnh0'.
C:\Program Files\MSBuild\Microsoft\WebDeployment\v8.0\Microsoft.WebDeployment.targets(474,9): error MSB6006: "aspnet_merge.exe" exited with code 1.
Done executing task "AspNetMerge" -- FAILED.
It seems that it even is not related to a number of modules.
The error doesn't make sense for me.