1) Ch. 6, v. 13: "Keitz kol bossor" The end for all flesh Rashi says that wherever we find adultery or idol worship destruction comes to the world and destroys the good with the bad. It is interesting to note that the next words of Rashi d.h. "Ki" are that their doom was sealed because of theft. This seems to contradict his previous words, that adultery or idol worship brings death.
2) Ch. 6, v. 17: "Hamabul mayim" The deluge of water The M.R. explains "chomos" as immoral behaviour in the monetary realm that was not outright theft. A person would have a large amount of bricks piled up at his building site. One person after another would take only one brick, an item whose value is almost negligible, and could surely not be retrieved in court. This continued until there was not a brick left, a monumental loss for the builder, but an insignificant theft by each brick snatcher. How was the "mabul" punishment in kind?
3) Ch. 7, v. 21: "Va'yigva v'chole ho'odom" Why did the minors deserve to die?
4) Ch. 8, v. 20: "Va'yaal olos" And he offered oloh sacrifices Why specifically "olos?"
5) Ch. 9, v. 23: "Va'yikach Shem voYefes es hasimloh" Shem and Yefes took the garment The gemara Sanhedrin 70a says that in the merit of Shem's taking the garment his descendants received the mitzvoh of "talis shel tzitzis." The gemara Chulin 89a seems to say otherwise. The merit for tzitzis is Avrohom's saying "Im michut v'ad sroch naal" (Breishis 14:23).