yamaguchi@,
Looks like it is related to the transition to overlay scrollbar?
Could you check if this still reproduces when you have a spare time?

I could see it in the latest build. Not yet verified by the old revisions, but I think this is not relevant to overlay scroll bar.

div.dialog-navigation-list
 div.dialog-navigation-list-footer
  div#progress-center
   #progress-center-open-view

Currently the dialog-navigation-list is set to overflow:hidden and only that box fits in the window. Other boxes inside it are larger than it (with enough number of LI items).

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/5c5f86f2c1fda2d9ec2b947aa7b44cea985f0d03

commit 5c5f86f2c1fda2d9ec2b947aa7b44cea985f0d03
Author: Joel Hockey <joelhockey@chromium.org>
Date: Fri Nov 23 04:32:05 2018

FilesApp progress center: allow scrolling of items

Bug:  627371 
Change-Id: I55e322bd36ff7eeb5699f9e2bd9842c01938d1da
Reviewed-on: https://chromium-review.googlesource.com/c/1349131
Reviewed-by: Stuart Langley <slangley@chromium.org>
Commit-Queue: Joel Hockey <joelhockey@chromium.org>
Cr-Commit-Position: refs/heads/master@{#610532}
[modify] https://crrev.com/5c5f86f2c1fda2d9ec2b947aa7b44cea985f0d03/chrome/browser/chromeos/file_manager/file_manager_uitest.cc
[modify] https://crrev.com/5c5f86f2c1fda2d9ec2b947aa7b44cea985f0d03/ui/file_manager/file_manager/foreground/css/file_manager.css
[modify] https://crrev.com/5c5f86f2c1fda2d9ec2b947aa7b44cea985f0d03/ui/file_manager/file_manager/test/BUILD.gn
[modify] https://crrev.com/5c5f86f2c1fda2d9ec2b947aa7b44cea985f0d03/ui/file_manager/file_manager/test/js/externs.js
[add] https://crrev.com/5c5f86f2c1fda2d9ec2b947aa7b44cea985f0d03/ui/file_manager/file_manager/test/progress_center.js

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/c2eb8a38f619ee905b8647a1e006d32009c2856c

commit c2eb8a38f619ee905b8647a1e006d32009c2856c
Author: Sam McNally <sammc@chromium.org>
Date: Tue Nov 27 11:36:41 2018

Fix Files App progress-center scrolling.

The old scrolling scrolled the entire footer; since the
progress-center-open-view is always present, but below the fold, this
allowed the progress-center-open-view to be scrolled off the top of the
footer element. Avoid this by only allowing scrolling on the
progress-center-open-view element. Additionally, restrict its height to
40% of the window so the directory tree can remain usable while the
progress center is expanded.

Slightly improve the position of notification dismiss buttons: align
them to flex-start instead of flex-end and use display: none for the
cancel button when hidden.

Bug:  627371 
No-try: true
Change-Id: I2180eb8382c37c1fc03ec32b4894f449f4c7a681
Reviewed-on: https://chromium-review.googlesource.com/c/1351202
Commit-Queue: Sam McNally <sammc@chromium.org>
Reviewed-by: Luciano Pacheco <lucmult@chromium.org>
Cr-Commit-Position: refs/heads/master@{#611068}
[modify] https://crrev.com/c2eb8a38f619ee905b8647a1e006d32009c2856c/ui/file_manager/file_manager/foreground/css/file_manager.css