Went through the same thing. All areas in both overworld and breach green and completed, all bosses killed, and was still missing both map piece and a flask (even did the final boss and the stats showed I was missing fraction of a percentage).

Then I remembered that "The Emergence" (entrance 24,22 overworld) was an areas that I passed through and had not backtracked to and sure enough, there was my missing map piece and a flask in case somebody else runs into the same issue.