The documentation of Merge includes:

It won't merge unexported (private) fields and will do recursively any exported field.

Yet in 0.3.9:

package main

import (
	"fmt"

	"github.com/imdario/mergo"
)

type inner struct {
	A int
}

type outer struct {
	inner
	B int
}

func main() {
	dst := outer{
		inner: inner{A: 1},
		B:     2,
	}

	src := outer{
		inner: inner{A: 10},
		B:     20,
	}

	err := mergo.MergeWithOverwrite(&dst, src)
	if err != nil {
		panic(err.Error())
	}
	fmt.Printf("%#v\n", dst)
}

and that used to be the case with 0.3.8, returning

main.outer{inner:main.inner{A:10}, B:20}

0.3.9 ignores the embedded struct entirely, returning

main.outer{inner:main.inner{A:1}, B:20}

Using a public name for the inner struct does cause the fields to be merged recursively.

AFAICS this was intentional or at least noticed, #105 (review) points to a test that broke and had to be changed, but there was no further rationale. But that doesn’t really say why this had to change.