“The OU stopped labeling the individual cups because it could be misleading. If someone used a non-kosher k-cup right before the person comes in with his/her k-cup, then the Keurig machine would not be kosher; thus the coffee also wouldn’t be kosher anymore.”
That doesn’t sound like a good reason to stop labeling the cups. It’s like saying they shouldn’t put a hechsher on cheese because someone might put it on a hamburger and then it wouldn’t be kosher anymore. I know it’s not exactly the same, but it’s the same idea. When they label a package, they are certifying that the product itself is kosher. There are always other kashrus considerations, and it’s your responsibility as a Jew to be aware of them.