I see this every day on pretty much every channel. Generally speaking, I pick up the right shows. There are, however, a few channels that will pick up every episode listed on an SP (for 'new only') even though the reruns are marked reruns. This can be a major PITA on cable channels, where episodes are re-run a zillion times.
I have pretty much given up trying to figure this one out, as it's been that way for years. There are a few of my shows that I just go through each week and manually set up the recording. It seems like some channels, like E! and Comedy Central, are the worst. I have to routinely go through my 'to do' list and delete reruns that are being auto-scheduled.