Shit that doesn't make any sense

What was the cake scene?

Why did Homura beg to die when her master plan was to replace Madoka? If she was dead wouldn't that stop her from saving Madoka?

Homura says she will maybe destroy the world once all the wraiths are destroyed. If the wraiths are manifestations of human despair and suffering, and Homura causes both, doesn't that mean she wont destroy the world?

If Madoka is omniscient and knows all timelines then wouldn't she know that Homura would eventually betray her? Even with the Incubator's distortion field preventing her from seeing inside, the Incubators were sitting around it. Couldn't Madoka see them?

Why did Madoka choose Bebe and Sayaka as her angels? Why not Sayaka, Mami, and Kyoko? Does she not like Kyoko and Mami? Why did she choose Bebe? Were the other witches a bunch of assholes?

Why could Sayaka transform into Octavia, let alone control it? Didn't Madoka's wish prevent all witches from being created, even retroactively?

If Homura brought people she knew and cared about into her witch realm, then why did she bring in Madoka's parents if she only talked to them for a little while at the end of Episode 12? Why did she bring in Hitomi and Kyousuke if she had never talked to either, let alone cared about them?

In Episode 9, Kyoko has to hold onto Homura in order to not be frozen in time. Why then can Mami move freely and fight Homura? She also would have had to transform at some point. If being transformed prevents you from being frozen and you can apparently do it freely, why didn't Madoka do the same? Why did Homura freeze time multiple times during the fight if she knew Mami was not affected? Why was Mami suddenly affected when Homura shoots herself?

Why did Mami shoot at Homura when it was shown multiple times that Homura was affected by her yellow ribbons?

If Madoka gave her memories to Sayaka and Bebe then wouldn't they have knowledge of the past and future? Wouldn't they know that Homura would try to replace Madoka in at least one universe?

What was Homura doing in a desert? At the end of the anime she was shown in the same desert. Did she go there to die? If she went there to die/become a witch then why didn't Madoka break her soul gem before she got there?

Why did Homura keep the Incubators around? Why didn't she just create a universe where entropy does not exist?

Why is Sayaka still a Magical Girl?