Found the issue.
In some templates I had this:
<h2>[[[[*isfolder:is=`1`:then=`$pagetitle`:else=`$parentpagetitle`]]]]</h2>
In the $pagetitle chunk I just had: [[*pagetitle]]
In the $parentpagetitle chunk I had:
[[#[[*parent]].pagetitle]]
Which is useable by
fastField.
When any pages that were either folders or children that used templates with this command they rendered. When they were not either, they did not.
I changed $parentpagetitle to:
[[getResourceField? &id=`[[UltimateParent]]` &field=`pagetitle`]]
Tried:
[[#[[UltimateParent]].pagetitle]]
But it didn't seem to work.