I was hoping that it was an easy thing like a text place holder on your slide master was sending some formatting information to your text box on the slides, but it's not that simple.
I don't see a reason for why this is happening, I know it's easily fixed and I'm not sure it has anything to do with the font since if you change the font the superscript formatting remains even on new bullets.
To fix it select all of your text and either right click for format Font... or click the down arrow in the lower right corner of the home > font ribbon section and deselect superscript. It not only removes it from the selected text but removes the formatting for the box so new bullets are formatted without Superscript.
I suspect something was pasted from a pre-formatted bit of text and it is causing these superscript issues.