The current generation of a .msi installer using WiX appears to create 'bundle.wxi' with custom code. This code lumps as many files into a single MSI Component as possible. That can be problematic as the component contents can change between versions while the key file remains unchanged, something not allowed according to MSI component rules.

WiX includes a tool, heat.exe, which can be used to build a WiX source file by harvesting a folder. It would be better to use heat.exe to harvest the application image.