In all cases that I have seen the "flipped" notes are more expensive than the ink smeared notes. Why is this? I know they are cool, but shouldn't the ink smeared issues be rarer?
Flipped like an inverted face/back? Or do you mean inverted overprints? They both cost more because they are rarer than ink smears, which are relatively common. Inverts require human errors. Better training can help alleviate them. The last couple of decades of currency have seen very few printing errors. The 1970s and 1980s were a very different story. It makes me wonder if everyone at the BEP was eating acid and mushrooms.
What is your interpretation of a "Flipper note"? If, what you mean is a direct or indirect transfer on the print to the opposite side, then it has to deal with a part of the process. Most are mechanical, and other are human. So, we need more information as to your question of 'flipped". Ink smears are from some of the cleaning, inking, oiling, processes of the equipment during the printing process.
For the rev to be in the opposite position to the obv. After the first printing, the backs have to have been placed in the feed elevator of the printing press in the wrong direction. The sheets have an ID on them for alinement to the press, so this should not happen, but some of the operators, do and make mistakes for whatever reason. The ID points are later removed from the currency,during the cutting process. Sometimes you will see on older currency with the cutting "cutting lines".