It's likely f.lux cannot ever do anything about it. Until Night Shift was available, I've been in the habit of of creating "low color temp" color profiles and manually setting my display to them when it gets late in the day (a crude approximation of f.lux, but ultimately the same thing they are doing). It always produced the same artifact.
Incidentally, I find it strange that f.lux is claiming they output so much less blue light than Apple's Night Shift, since as far as I can tell, all they do is shift the color profile, just like Night Shift does. Anyone who has seen the video issues I'm describing above can attest that there is still plenty of blue light coming out of the screen with f.lux (and manual color profile adjustments). All three accomplish the same thing, it's just that Apple's implementation appears to be cleaner and work in more cases (not surprising -- it's their system, so presumably they know how to integrate with it better than anyone). I think perhaps at most they have a point that the default settings are maybe not "warm" enough, but that's the only flaw I can see.
I've had the same issue with an Intel GPU'ed MBPR 13" (ie, no Radeon or Nvidia GPU also), and it rarely happened in OSX, but only during certain HW accelerated overlays (such as YUV acceleration in videos, or OpenGL programs doing sufficiently interesting things).
I don't think F.lux has the bug, but OSX's rendering pipeline does. I had similar issues with color profiles I generated myself that noticeably differed from the screen itself (Apple has yet to produce an actually fucking accurate-to-sRGB screen, I don't care how many Photoshop jockeys praise their lord and savior, St. Jobs).
So, yeah. In other news, my MBPr runs Windows 10 and I'm never going back; and I've also never seen the bug here.
The side effect is: F.lux's Windows version is not feature complete with OSX's, and noticeably redshifts at different times than OSX does depending on what settings you prefer.
https://forum.justgetflux.com/topic/58/strange-colors-blue-f...
(Also if you have an external display connected, "integrated only mode" is ignored in gfx).
But I usually just leave my mouse over the Mac menu bar.