"Collect Files..." collecting additional unwanted comps

Hey so I use "Collect Files" all the time. I collaborate with other people and this function is obviously vital.
I'm currently having an issue with it collecting comps that are not selected. I choose "For Selected Comps" and I check off "Reduce Project." The new file has the comp I want, but also others. And if I try another comp, it will collect the same additional ones each time. And In the generated report, it is listing the comps I don't want as collected.
It seems to be specific though, collecting comps that are from other .aep files that I've imported. And only comps from .aep files that where generated with Collect Files. In other words, basically anything I've round-tripped using Collect Files and imported after a collaborator has finished their work.
I'm using AE 12.0.0.404 and I'm on OSX 10.8.4
Anyone else experiencing this problem? Or know if I'm missing something, like some sort of option/toggle that will force the collection of a comp? Thoughts?
Thank you!

If I duplicate the unwanted comps and delete the originals, it no longer collects when not selected... Weird. Simple workaround, but would still love to know what's going on if anyone has an idea. Thanks.

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