Difficulty with Color Themes

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After deciding to make my own custom color theme (I know where the options are to create one, that isn't what this post is about) I noticed that several of my apps have their icons turned black and white (Mail, Settings, etc.) and I don't know how to change them back to the default colored version. Also, several random things have changed on Chrome (my browser of choice). Lots of random buttons, text, and the like have things like boxes around them, the formatting on several sites I frequently use is all messed up, and I don't know if there's a way to make my selection for a color theme less i

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