Aperture Imports Duplicates and Triplicates of Photos from my iPhone 6 Plus

When I import photos from my iPhone 6 Plus, Aperture imports duplicates and triplicates of the identical photo randomly. This results in hours of going back through all of the Projects in Aperture and manually deleting the duplicates.
I thought that maybe I was mistaking standard and HDR versions of the same photo, or even burst shots that looked very similar, but this isn't the case. It is the same file name followed by a (1), (2), and sometimes a (3). I also know this isn't the case, because my Camera Roll has about 1,200 photos and videos on it (I stopped importing photos to my hard drive a while ago because of the duplicates, hoping an update would come out to fix the problem), but Aperture tells me that it is going to import over 4,000 photos from my iPhone 6 Plus, not the 1,200 that is on it. This is because of a bug that is double and triple counting many of the photos and videos.
Interestingly enough, Image Capture recognizes only the 1,200 photos on the iPhone, but I'm reluctant to use it because it won't append the Metadata that I have preset in Aperture or automatically run the preset enhancements. I also don't use Image Capture so I'm not sure if it might leave out any Metadata or have some other drawback that I'm not aware of.
So far I've don't he standard troubleshooting, have restarted my iMac and iPhone 6 Plus, ran repair permissions, waited for an update, etc. but I still have the same problem.
I've all but given up on Aperture and am waiting anxiously for the Apple to release the new Photos software, but I need to spend time to work around this bug before then. I can't leave this many photos and videos on my iPhone and need to get them imported into Aperture.
Is there an obvious fix to this that I'm overlooking?

Interestingly enough, Image Capture recognizes only the 1,200 photos on the iPhone, but I'm reluctant to use it because it won't append the Metadata that I have preset in Aperture or automatically run the preset enhancements. I also don't use Image Capture so I'm not sure if it might leave out any Metadata or have some other drawback that I'm not aware of.
If Image Capture imports correctly, use it to import to a folder and then import that folder to Aperture. You can use the same presets when importing from a folder as when importing from a camera of iPhone.
The same buggy behavior has been reported for iPhoto, since the iOS 8.1 release. It happens in iPhoto, Image Capture, Aperture, but not all are seeing this problem.
For example, see these discussions:
iPhoto Yosemite duplicates Photos while importing from iPhone
iPhoto 9.6 shows duplicate photos present on iPhone
Connecting iPhone duplicates photos in iPhoto
duplicate photos in camera roll on iPhoto
Unfortunately, there is no clear picture yet, what circumstances will make it happen, and how to prevent it.
For some forum members it was the Photo Stream (Duplication upon importation from Iphone to Iphoto), others found it was caused by HDR photos, for some the problem went away after the 8.1.2 update, for others it started with this update.
A few forum members reported, that it helped to dismount the iPhone and plug it in again (iPhoto 9.6 shows duplicate photos present on iPhone), and then the duplicates went away. One member reported, that Apple Support claimed this problem to be caused by iCloud iPhoto libary (Beta), and indeed turning off iCloud iPhoto libary (Beta) made he duplicates vanish for him.

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Aperture Imports Duplicates and Triplicates of Photos from my iPhone 6 Plus

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