Perhaps this is user error, but I noticed that running the following query when using makeExecutableSchema, the error coming back is connected to the BookInput type.

mutation {
    createAuthor(input: {
        name: "M"
    })
}

Here's a repo both with and without makeExecutableSchema used:
https://github.com/morleytatro/graphql-tools-bug

Notice the difference in results.