I just had a look and it looks like this is caused by this CL:
https://chromium.googlesource.com/chromium/src/+/7d8ce7003186698ce565f6eb59bf7027a2707f22

This line in particular is causing the issue:
https://cs.chromium.org/chromium/src/chrome/browser/ui/cocoa/omnibox/omnibox_popup_matrix.mm?rcl=0&l=50

Basically we're explicitly ignoring the fact that it's in dark mode.
I guess this is now an outdated design?

Moving this nonessential bug to the next milestone.

For more details visit https://www.chromium.org/issue-tracking/autotriage - Your friendly Sheriffbot

Ah, so the fix should be as simple as telling it not to ignore dark theme?

You talked about an outdated design - what are you referring to?

Yeah, that should be it. I was actually asking if ignoring the dark mode was part of an older Material design spec. I want to make sure if it's okay for us to get rid of

It sounds like you're saying there might be code that's no longer needed. If so, that can definitely be removed.

Awesome thanks! I'll go ahead and remove it

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/a8403516d197bb546c068d3202f41844a004892e

commit a8403516d197bb546c068d3202f41844a004892e
Author: spqchan <spqchan@chromium.org>
Date: Wed Jun 29 01:46:11 2016

[Material][Mac] Set Incognito Omnibox Dropdown Icons to White

BUG= 618763 

Review-Url: https://codereview.chromium.org/2082723002
Cr-Commit-Position: refs/heads/master@{#402634}

[modify] https://crrev.com/a8403516d197bb546c068d3202f41844a004892e/chrome/browser/ui/cocoa/omnibox/omnibox_popup_matrix.mm
[modify] https://crrev.com/a8403516d197bb546c068d3202f41844a004892e/chrome/browser/ui/cocoa/omnibox/omnibox_popup_view_mac.h
[modify] https://crrev.com/a8403516d197bb546c068d3202f41844a004892e/chrome/browser/ui/cocoa/omnibox/omnibox_popup_view_mac.mm

Your change meets the bar and is auto-approved for M52 (branch: 2743)

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/caeb412303073d89f6a6384798eed1ad2b691494

commit caeb412303073d89f6a6384798eed1ad2b691494
Author: spqchan <spqchan@chromium.org>
Date: Thu Jun 30 01:01:05 2016

[Material][Mac] Set Incognito Omnibox Dropdown Icons to White

BUG= 618763 

Review-Url: https://codereview.chromium.org/2082723002
Cr-Commit-Position: refs/heads/master@{#402634}
(cherry picked from commit a8403516d197bb546c068d3202f41844a004892e)

Review URL: https://codereview.chromium.org/2105413003 .

Cr-Commit-Position: refs/branch-heads/2743@{#539}
Cr-Branched-From: 2b3ae3b8090361f8af5a611712fc1a5ab2de53cb-refs/heads/master@{#394939}

[modify] https://crrev.com/caeb412303073d89f6a6384798eed1ad2b691494/chrome/browser/ui/cocoa/omnibox/omnibox_popup_matrix.mm
[modify] https://crrev.com/caeb412303073d89f6a6384798eed1ad2b691494/chrome/browser/ui/cocoa/omnibox/omnibox_popup_view_mac.h
[modify] https://crrev.com/caeb412303073d89f6a6384798eed1ad2b691494/chrome/browser/ui/cocoa/omnibox/omnibox_popup_view_mac.mm

Tested the above issue on Mac 10.11.5 with chrome version '52.0..2743.75' & omnibox  drop down icons are white in incognito. Hence marking the same as TE-Verified-52.0..2743.75.

Thank you!