Which version are you testing on?  I thought this was fixed in revision 2d431caf4acd0d16ed8d0c13808466016653729e.

I'm testing on tip of tree, can still repro the issue.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/52ae461c5425a13fa7a2559dea28bb208ef0dc87

commit 52ae461c5425a13fa7a2559dea28bb208ef0dc87
Author: Scott Chen <scottchen@chromium.org>
Date: Thu Aug 03 00:52:23 2017

MD Extensions: fix subpage height and scroll issues.

The subpage's main container is too short and contents are leaking out of it. This CL makes it such that the main-container spans full height and puts the overflow scrolling on the parent detail-view element.

Bug:  741226 
Cq-Include-Trybots: master.tryserver.chromium.linux:closure_compilation
Change-Id: Ic0fe061435bc82544058533126e5eba75be8f357
Reviewed-on: https://chromium-review.googlesource.com/598504
Reviewed-by: Devlin <rdevlin.cronin@chromium.org>
Commit-Queue: Scott Chen <scottchen@chromium.org>
Cr-Commit-Position: refs/heads/master@{#491575}
[modify] https://crrev.com/52ae461c5425a13fa7a2559dea28bb208ef0dc87/chrome/browser/resources/md_extensions/detail_view.html

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/0364bdbc54c2829fb1d8acf8d1c2120083d31481

commit 0364bdbc54c2829fb1d8acf8d1c2120083d31481
Author: Scott Chen <scottchen@chromium.org>
Date: Thu Aug 03 21:50:56 2017

MD Extension: full subpage height.

Follow up of 598504 (missed committing a change that I made locally).

Bug:  741226 
Cq-Include-Trybots: master.tryserver.chromium.linux:closure_compilation
Change-Id: I03848ef5dd9c9207262c2d48f491d678980e2b9c
Reviewed-on: https://chromium-review.googlesource.com/599221
Reviewed-by: Demetrios Papadopoulos <dpapad@chromium.org>
Commit-Queue: Scott Chen <scottchen@chromium.org>
Cr-Commit-Position: refs/heads/master@{#491854}
[modify] https://crrev.com/0364bdbc54c2829fb1d8acf8d1c2120083d31481/chrome/browser/resources/md_extensions/detail_view.html