Media Encoder makes duplicate proxies

I have a huge library of 4K footage for a project I'm working on. All of the clips are spearated into bins for ease of identification. Some clips are from the same original video file, so when I got to create proxies of all my individual clips, media encoder creates a duplicate proxy of the entire original video file.

e.g. 

"Video File A" has two clips I've identified that are in two separate bins. During Proxy creation, media encoder makes two proxies for "Video File A"

Is there a way to avoid this happening?