Bug? macOS Sierra Preview/Quick Look issues with rendering colors of images when using any icc profile other than the macOS standard
(After reading all the literature I could find around the issue here's what I've learned)

A disclaimer first

There is a chance (as @Mr.Kennedy points out) that your system is suffering from issues with the quicklook generator. You may wish to read first his very thorough details on clearing the cache and debugging qlamanager's process of generating the thumbnails/previews. If you are certain the actual thumbnails/previews generated are fine, read on!

the Problem

Description of the problem

Apple programs and programs that depend on ColorSync CMM's capabilities, exhibit under some conditions crushed black colors and gamma issues.

Programs affected


Preview
Quick Look (when zoomed in)
Certain versions of Lightroom
The Export As... preview at Photoshop (the Save for Web (legacy) dialog is not affected on the other hand)
Apple Photos App
Apple iPhotos App
Aperture
Quicktime
Finalcut Pro X


(the issues affecting QT, FCPX Lr and Aperture may be different, I'm not sure)

Programs (not) affected


Quick Look (before zooming in)
Finder previews/thumbnails
Adobe Bridge
all programs who manage their own colors


Specifics

This is an issue (or a family of issues) around ColorSync. Most probably an Apple's bug inside ColorSync or Preview/QuickLook/Photos, that affects some color profiles generated by a few profiling software, but does not affect other profiles at all (such as the factory profiles).

According to some, first ColorSync issues were introduced in Mountain Lion. Others had issues in Mavericks, while others discovered it first in El Capitan. I can verify that it is still present in Sierra though. It's unclear if all these issues were all one and the same, but in here I'll treat them as such.

Adobe is aware of these issues (it was affecting Lightroom up to some version) rectified it since(2), but consequent updates by apple have complicated things since it has reemerged in a different way. There is a lengthy discussion in the Adobe forums(3).

Cause

At the root, it is that certain ICC profiles, contain information that **Apple's ColorSync won't treat properly (and this affects all programs that rely on ColorSync).
There have been various ideas proposed as what it is that ColorSync doesn't like about them.
This issue has been linked (but inconclusively) to:


LUT based icc profiles
matrix based icc profiles
particular software used to generated the ICC profile (eg displayCal/basICColors).
compatibility issues with the ICC version number (ICCv2 or v4 profiles)
black point compensation accounted for in the profile curves.
EIZO displays
Secondary displays


There has been no consensus though. For instance I've seen both ICCv2 and ICCv4 profiles that work, and ICCv2 and ICCv4 profiles that do not.

Solution

No solution has been found yet afaik.


From reports, it seems that profiles created with certain programs seem to be "incompatible" while profiles created by other programs seem to be fine.If you are using 


displayCal (using ArgyllCMS) (aka dispcalGUI)
basICColor 
Eizo ColorNavigator (4)


this may be the related. testing some other software for profiling, may be the solution for some who have the option
Others have reported success with experimenting by changing parameters of the profiles generated (ICC version number, black point compensation, LUT, curves, 3x3 matrix) but nothing definitive.
Adobe is implementing its own workarounds(2),(5) (that seem to be falling apart when apple is changing something).
One could revert to using the factory profile (for those who don't care about color management) which work fine
Needless to say that avoiding ColorSync reliance and using programs that color manage their own output everywhere in your work environment is certainly the most complete solution (but rarely a viable option)


Raising Awareness

You may also wish to add your voice by submitting to Apple a bug report on the issue

Other places where this problem is discussed

I'm listing here some of the other places where these issues are being discussed

OSX Preview issues


Q: Preview+El Capitan = color management bug?
Q: wrong colors in preview.app
Dark Images in Mac "Photos" &amp; "Preview" with DisplayCAL generated Profile


Adobe Lightroom


Lightroom 5 ICC profiles clipped shadows under OSX
Serious color management bug in Mac OS 10.9 "Mavericks"
Further quantification of the Mavericks color management problem


Finalcut Pro X


Q: Very very dark video in FCP X viewer.