I talked to a Autodesk tech about the issue 3-4 months ago and it won't be "fixed" because they don't see it as being broken. Basically its our fault that the load collections feature is enabled by default and we neglect to turn it off... awesome logic... Let me explain.
Each time you load a scene that contains a biped with collections and the "load collections is turned on" it will load the collections even if they are exact dupes (that last part I consider a bug). You can sit there opening/saving the same file over and over again chunking up the file size because it keeps adding the same collection each time. Now imagine what it does when you've loaded a file with 1 collection 50 times? Thats right kids you now have 50 collections and the next time you save/open the file, you now have 100.
Sounds like a bug to me so far, but they do this so you can keep working in the same instance of Max and use the collection(s) on any biped created, merged, or imported into Max while it is open. They aren't necessarily scene/file/Biped specific any more. It doesn't require you to manually save and load collections which CAN be handy when working with many different bipeds (like say a crowded scene or large flocks of characters). It would be insanely time consuming to update all the collections for each biped by the traditional save/load commands. I'm sure it can be scripted but they where being nice and gave us this wonderful "feature" and left it enabled, which pisses everyone off that doesn't need it, us single character folks.
He did admit that its redundant and costly, when it imports identical collections and said he would pass that info along. We'll see if it actually stops doing it soon enough.
This feature pisses a lot of people off.