Now this is interesting. Seems that some of you who have purchased apps from the Amazon Appstore are starting to see conflicts with the Android Market. A couple scenarios appear to be playing out. In some instances, the Android Market sees an app that was purchased from the Amazon Appstore, knows an updated version is available, but then fails on updating because the app wasn't actually purchased from the Android Market. While we're not exactly sure what's going on, it may be an issue where some developers use the same signing key for applications in both the Android Market and other app stores. This could cause your phone or tablet to see the applications as identical. That's just a hunch, and chances are Google has a better grasp of the situation than we do.
Reversing things, as TWiT's Jason Howell points out, the Amazon Appstore can see that you have an app installed and offer to unassociate it from that other market so that you can get updates and such through its services instead. How handy. But it also smells of someone standing next to your car in a parking lot, pointing out a dent you know wasn't there when you left your car, and then recommending a friend who can fix it on the cheap. There's just something offputting about it.
This could end up being an interesting push and pull, but we've got a feeling Google's got the upper hand here, being able to more easily and quickly tweak code to keep things in line. And as violent23 points out in our forums, Google's already aware of this and is on the case. Should be interesting to see how it all works out.