Reported in the forums:

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It looks like the problem was actually in the version specified in fx:application

C:\Users\me\AppData\Local\Temp\build5821836786331875470.fxbundler\windows\remus.wxs(4) : error CNDL0108 : The Product/@Version attribute's value, '1.0.0-alpha', is not a valid version. Legal version values should look like 'x.x.x.x' where x is an integer from 0 to 65534.
C:\Users\me\AppData\Local\Temp\build5821836786331875470.fxbundler\windows\remus.wxs(4) : error CNDL0010 : The Product/@Version attribute was not found; it is required.

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Make sense to add code to ignore version or at least validate and skip bundler.
And we need to document it too.