I believe the issue is with the if condition checking for playedTime in  callPauseIfTimeIsReached() in video.js file [1].
[1]: https://cs.chromium.org/chromium/src/third_party/WebKit/LayoutTests/media/video-played.js?q=video-played.js&sq=package:chromium&g=0&l=41

Looks like somehow the playedTime is coming 0 in mac build.
Just added the below test code before that if condition and I am able to simulate the issue in linux build.
***************************
if (playedTime < 0)
  playedTime = 0;
***************************

And changing the condition to "if (playedTime <= 0)" is fixing the issue.
I will push the patch after verification of media tests locally.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/568f9653141a1b144cdf0de33cb03450e6f53557

commit 568f9653141a1b144cdf0de33cb03450e6f53557
Author: Sriram <srirama.m@samsung.com>
Date: Mon Aug 20 12:57:46 2018

Fix flakiness for media/video-played-collapse.html

The failure is very rare but there is one on the Mac build [1].
There is a possibility of playedTime being 0 in callPauseIfTimeIsReached()
in video-played.js file which i believe is hitting in this case.
[1]: https://ci.chromium.org/p/chromium/builders/luci.chromium.ci/Mac10.13%20Tests/4724

BUG= 874799 

Change-Id: Iffe3ac49d20664eb9f824e2a1dd24aaa371dcbb2
Reviewed-on: https://chromium-review.googlesource.com/1181007
Reviewed-by: Fredrik Söderquist <fs@opera.com>
Commit-Queue: srirama chandra sekhar <srirama.m@samsung.com>
Cr-Commit-Position: refs/heads/master@{#584415}
[modify] https://crrev.com/568f9653141a1b144cdf0de33cb03450e6f53557/third_party/WebKit/LayoutTests/media/video-played.js

I hope this is fixed now. Marking it as fixed.