Able to reproduce the issue on Mac10.12.2 and below are the per revision bisect details for the same:

Good build:57.0.2958.0--Revision-439976
Bad build:57.0.2959.0--Revision-440307

You are probably looking for a change made after 440205 (known good), but no later than 440206 (first known bad).
CHANGELOG URL:
The script might not always return single CL as suspectas some perf builds might get missing due to failure.
  https://chromium.googlesource.com/chromium/src/+log/81a0e72b623acb1710b279d072ba0272ad8234bf..fdc6c66162e754b82e2d7f5db09767733d49005c

Possible suspect:
https://chromium.googlesource.com/chromium/src/+/fdc6c66162e754b82e2d7f5db09767733d49005c

Review-Url: https://codereview.chromium.org/2594543004

lgrey@ Assigning to you, kindly have a look into it.

Thanks.

A friendly reminder that M57 Stable is launch is coming soon! Your bug is labelled as Stable ReleaseBlock, pls make sure to land the fix and get it merged into the release branch ASAP so it gets enough baking time in Beta (before Stable promotion). Thank you!

sdy@ and thakis@ (possible suspect CL reviewers - https://codereview.chromium.org/2594543004), can anyone of you PTAL as this bug is marked as M57 Stable blocker and lgrey@ is OOO Parental Leave. Thank you.

Looking.

I can't reproduce this on Canary (58.0.3007.0) or on the specific revision mentioned in #1 (57.0.2959.0). I'm going to keep trying, but am I doing something wrong? Screen recording attached.

Deleted: permission_bubble_alignment_wfm.mov 4.8 MB

permission_bubble_alignment_wfm.mov 4.8 MB Download

sdy@: Please refer the attached screen cast for the reproducing the issue.
Issue persists in Canary 58.0.3013.0 and Beta 57.0.2987.54.

Deleted: 687079_Feb_16.mp4 870 KB

	687079_Feb_16.mp4 870 KB View Download

A friendly reminder that M57 Stable is launch is coming VERY soon! Your bug is labelled as Stable ReleaseBlock, pls make sure to land the fix and get it merged into the release branch (2987) ASAP so it gets enough baking time in Beta (before Stable promotion). Thank you!

Back to triage given that lgrey is away and this is releaseblock-stable

I can deal with this, just verifying the regression.

lgrey@ is back \o/.

URGENT - PTAL ASAP.

We're getting VERY close to M57 Stable promotion. And 
this issue is marked as M57 stable release blocker. Pls make sure to land the fix and get it merged into the release branch ASAP so it gets enough baking time in Beta (before Stable promotion).

Know that this issue shouldn't block the release?  Remove the ReleaseBlock-Stable label or move to M58.

Thank you.

Sorry for the delay on this, I just got back from parental leave yesterday.

There's a fix waiting on owner's review at https://codereview.chromium.org/2706273004/

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/ac719a4ad8dd599eea270444f37a3cc3a05be4a5

commit ac719a4ad8dd599eea270444f37a3cc3a05be4a5
Author: lgrey <lgrey@chromium.org>
Date: Wed Feb 22 19:16:57 2017

[Mac] Fix bubble origin for animated Omnibox decorations

Conceptually similar to the code removed in https://codereview.chromium.org/2594543004
but now takes padding into account so that the arrow isn't offset.

BUG= 687079 

Review-Url: https://codereview.chromium.org/2706273004
Cr-Commit-Position: refs/heads/master@{#452160}

[modify] https://crrev.com/ac719a4ad8dd599eea270444f37a3cc3a05be4a5/chrome/browser/ui/cocoa/location_bar/content_setting_decoration.mm

Verified this issue on Mac OS 10.12 using chrome latest Dev M58-58.0.3021.0 by following steps mentioned in the original comment, Observed the popup blocker bubble is aligned properly as expected. Hence adding TE-Verified label for M57.

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	687079.mp4 645 KB View Download

Your change meets the bar and is auto-approved for M57. Please go ahead and merge the CL to branch 2987 manually. Please contact milestone owner if you have questions.
Owners: amineer@(clank), cmasso@(bling), ketakid@(cros), govind@(desktop)

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

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/eb17964584d04aecd6c3fd8217c6f0d1d4313831

commit eb17964584d04aecd6c3fd8217c6f0d1d4313831
Author: Sidney San Martín <sdy@chromium.org>
Date: Thu Feb 23 19:33:28 2017

[Mac] Fix bubble origin for animated Omnibox decorations

Conceptually similar to the code removed in https://codereview.chromium.org/2594543004
but now takes padding into account so that the arrow isn't offset.

BUG= 687079 

Review-Url: https://codereview.chromium.org/2706273004
Cr-Commit-Position: refs/heads/master@{#452160}
(cherry picked from commit ac719a4ad8dd599eea270444f37a3cc3a05be4a5)

Review-Url: https://codereview.chromium.org/2716503005 .
Cr-Commit-Position: refs/branch-heads/2987@{#664}
Cr-Branched-From: ad51088c0e8776e8dcd963dbe752c4035ba6dab6-refs/heads/master@{#444943}

[modify] https://crrev.com/eb17964584d04aecd6c3fd8217c6f0d1d4313831/chrome/browser/ui/cocoa/location_bar/content_setting_decoration.mm

Verified the issue on Mac 10.12.3 and 57.0.2987.88 its working fine now.
Please find the screen cast for the same.
Hence added respective TE-verified labels to it.

sdy@/lgrey@: Could you please update the status to Fixed/Verified.

Deleted: 687079_Mar_1.mp4 558 KB

	687079_Mar_1.mp4 558 KB View Download