This is because of how the script that looks for buttons to click tries to look inside iframes as well:
https://cs.chromium.org/chromium/src/third_party/WebKit/LayoutTests/external/wpt_automation/fullscreen/auto-click.js

The test themselves are manual and not wrong, but the automation script assumes that it's possible to access iframe.contentDocument.

kereliuk@, this would require getting testdriver.click() working with fullscreen. Do we have a writeup of what didn't work when you tried? I believe the problem is upstream, where being in fullscreen meant that it wasn't possible to get events to the right window? If this is a wpt infra limitation we should have a bug there, and if it's a WebDriver limitation we should have a spec bug.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/961c6c6cc919c92c4a8e4c51656646730c2a344c

commit 961c6c6cc919c92c4a8e4c51656646730c2a344c
Author: Lukasz Anforowicz <lukasza@chromium.org>
Date: Mon Mar 12 21:24:17 2018

Triaging layout test failures from FlagExpectations/site-per-process

http/tests/devtools/appcache/appcache-iframe-manifests.js:
- This test was associated with crbug.com/678481 and that
  bug is now fixed, and the test-related expectation has
  already been removed from LayoutTests/TestExpectations
  in r527386

http/tests/media/autoplay/document-user-activation-*
- These tests are flaky regardless of site-per-process
  and are already covered by LayoutTests/TestExpectations.
  This CL just extends TestExpectations entry to also cover Win.

external/wpt/payment-request/allowpaymentrequest/setting-allowpaymentrequest-timing.https.sub.html
- New bug has been opened prior to this CL: https://crbug.com/819800

external/wpt/fullscreen/api/element-ready-check*
- New bug has been opened prior to this CL:  https://crbug.com/820617 

external/wpt/css/css-fonts/font-display/font-display.html
- This test is simply slow and often takes more than 5 seconds to
  finish - see https://crbug.com/816026#c7
- The timeout of this test is (since 2018-03-12) covered by the main
  LayoutTests/TestExpectations (see r542490).

Other entries removed by this CL simply seem to have "healed" themselves
and are currently passing on the waterfall and on the tryjobs.

Bug: 477150,  794631 , 678481,  788390 
Bug: 819800,  820617 ,  788390 ,  801992 
Change-Id: If24ec321df9593ab217f50b7f1b39b3496faceef
Reviewed-on: https://chromium-review.googlesource.com/957683
Commit-Queue: Łukasz Anforowicz <lukasza@chromium.org>
Reviewed-by: Alex Moshchuk <alexmos@chromium.org>
Cr-Commit-Position: refs/heads/master@{#542601}
[modify] https://crrev.com/961c6c6cc919c92c4a8e4c51656646730c2a344c/third_party/WebKit/LayoutTests/FlagExpectations/site-per-process
[modify] https://crrev.com/961c6c6cc919c92c4a8e4c51656646730c2a344c/third_party/WebKit/LayoutTests/TestExpectations

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/1321da9b9650908ea060e2a40f25ef3bb01bfcdd

commit 1321da9b9650908ea060e2a40f25ef3bb01bfcdd
Author: Dave Tapuska <dtapuska@chromium.org>
Date: Tue Aug 28 22:14:43 2018

Remove fullscreen expectations for site per process.

https://chromium-review.googlesource.com/c/chromium/src/+/868323
fixed auto-click.js which fixed the errors for these tests in
site-per-process mode.

BUG= 820617 

Change-Id: Ib17d02b3aeb5af183cae2d8cfb7e141d8cbdcc8e
Reviewed-on: https://chromium-review.googlesource.com/1194733
Reviewed-by: Mustaq Ahmed <mustaq@chromium.org>
Commit-Queue: Dave Tapuska <dtapuska@chromium.org>
Cr-Commit-Position: refs/heads/master@{#586884}
[modify] https://crrev.com/1321da9b9650908ea060e2a40f25ef3bb01bfcdd/third_party/WebKit/LayoutTests/FlagExpectations/site-per-process