After changing the pads on a 2008 si I noticed halfway through that the upper and lower slide pins were different. The lower ones were round while the upper ones had flat spots. Anyone know why this is, and if its bad to mix them up?

 

Ask Honda why it is. And why would you want to mix them up? Did you not pay attention to what you were doing when you maybe reassembled them? Just wondering why you need to ask since you gave no back story whatsoever.