Launcher shows applications from OTHER partition

My iMac's 2011 internal disk is partitioned so that it can boot either with Mountain Lion, or Lion, depending on my needs.
I've just noticed that my Mountain Lion 10.8.2 Launcher shows certain applications that do not exist on my Mountain Lion partition, but do exist on my Lion partition.
Here's another observation : when I update my Mac App Store apps through Software Update in ML, I sometimes have to run it twice !
I figured that it first updates a given app that resides on my Mountain Lion partition, and then, at the next Software Update call, it will update the same app on my Lion partition.
I always thought that there was a certain "water-tightness" between partitions on a disk. Now I see it is not the case.
And I'm not sure that this is a "feature". I wonder if this can lead to problems. For example, if an app is compatible with Mountain Lion and not compatible with Lion, it could still be installed in Lion.
How about ejecting the irrelevant partition before Software Updating ?
Any thoughts ?
Thanks !
YM

Whether in your case with multiple OS X partitions, or in my case, with dual internal drives, the Dock on the primary drive will try resolve previous links to /Applications locations from previous preference settings.
Two things that I observed.
Spotlight was happy to index both drives at a performance loss.
The App Store may get confused about multiple Apple ID in multiple keychains.Which messes up normal App Store and Software updates.
In Spotlight > Privacy, I told it to ignore everything but the current boot drive.
I also created a new /etc/fstab file entry that blocked automounting the non-boot drive.
I then added missing apps back to the primary boot drive.

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