I think this is WAI.
Gray color indicates that the files are selected but the list view doesn't have keyboard focus. I think it is a necessary visual feedback as the user can use keyboard and touch (plus mouse) simultaneously.

I see. The focus doesn't come back even if I tap more files after tapping the action bar though. I can keep selecting files, but they get added with gray highlights. That doesn't seem right?

Thanks, that makes much sense. I confirmed it also happens when doing the same before the long-tap to select first file.
So I think the issue is that tapping operations doesn't move the focus to the file list.

 Issue 752389  is similar to this issue.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/314eb17f4f278c9db669525137df44a5f27ca526

commit 314eb17f4f278c9db669525137df44a5f27ca526
Author: Tatsuhisa Yamaguchi <yamaguchi@chromium.org>
Date: Wed Aug 23 01:40:23 2017

Focus parent list element when tapped.

This will also allow to finish renaming when tapping outside the input
text box.

Bug:  755774 , 756839 
Cq-Include-Trybots: master.tryserver.chromium.linux:closure_compilation
Change-Id: I9d05724e85c9615b284dc7e799cb2dfb7f18f190
Reviewed-on: https://chromium-review.googlesource.com/622332
Commit-Queue: Tatsuhisa Yamaguchi <yamaguchi@chromium.org>
Reviewed-by: Naoki Fukino <fukino@chromium.org>
Cr-Commit-Position: refs/heads/master@{#496550}
[modify] https://crrev.com/314eb17f4f278c9db669525137df44a5f27ca526/ui/file_manager/file_manager/foreground/js/ui/file_grid.js
[modify] https://crrev.com/314eb17f4f278c9db669525137df44a5f27ca526/ui/file_manager/file_manager/foreground/js/ui/file_table_list.js
[modify] https://crrev.com/314eb17f4f278c9db669525137df44a5f27ca526/ui/file_manager/file_manager/foreground/js/ui/file_tap_handler.js

The change has been merged to master. merge-request to M61 is being done in 756839.

The steps to reproduce and verify the issue was changed a bit:
(1) Select one file in files app. See the selected file is highlighted blue.
(2) Tap the toolbar / action bar. See the highlight of the selected file turns gray.
(3) Tap another file in the list.
(4) Hit [up arrow] or [down arrow] keys.

Expected:
(3) The selected files stay selected with a blue highlight.
(4) Arrow keys cancel the selection and move focus between files.

What happened before the change:
(3) The highlight stays gray.
(4) Arrow keys do nothing.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/4a97cabaedd6e5aa1ac1d53317594e3835b9ea83

commit 4a97cabaedd6e5aa1ac1d53317594e3835b9ea83
Author: Tatsuhisa Yamaguchi <yamaguchi@chromium.org>
Date: Fri Aug 25 03:14:26 2017

Focus parent list element when tapped.

This will also allow to finish renaming when tapping outside the input
text box.

TBR=yamaguchi@chromium.org

(cherry picked from commit 314eb17f4f278c9db669525137df44a5f27ca526)

Bug:  755774 , 756839 
Cq-Include-Trybots: master.tryserver.chromium.linux:closure_compilation
Change-Id: I9d05724e85c9615b284dc7e799cb2dfb7f18f190
Reviewed-on: https://chromium-review.googlesource.com/622332
Commit-Queue: Tatsuhisa Yamaguchi <yamaguchi@chromium.org>
Reviewed-by: Naoki Fukino <fukino@chromium.org>
Cr-Original-Commit-Position: refs/heads/master@{#496550}
Reviewed-on: https://chromium-review.googlesource.com/634024
Reviewed-by: Tatsuhisa Yamaguchi <yamaguchi@chromium.org>
Cr-Commit-Position: refs/branch-heads/3163@{#870}
Cr-Branched-From: ff259bab28b35d242e10186cd63af7ed404fae0d-refs/heads/master@{#488528}
[modify] https://crrev.com/4a97cabaedd6e5aa1ac1d53317594e3835b9ea83/ui/file_manager/file_manager/foreground/js/ui/file_grid.js
[modify] https://crrev.com/4a97cabaedd6e5aa1ac1d53317594e3835b9ea83/ui/file_manager/file_manager/foreground/js/ui/file_table_list.js
[modify] https://crrev.com/4a97cabaedd6e5aa1ac1d53317594e3835b9ea83/ui/file_manager/file_manager/foreground/js/ui/file_tap_handler.js