Steps to reproduce the issue

form.xml

<?xml version="1.0" encoding="utf-8"?>
<form>
    <field 
        name="uploads"
        type="subform"
        formsource="path/to/subform.xml"
        label="" 
        description="" 
    />
</form>

subform.xml

<?xml version="1.0" encoding="utf-8"?>
<form>
    <field 
        name="fileupload" 
        type="file" 
        required="true" 
        label="" 
        description="" 
    />
</form>

model.php

$data = JFactory::getApplication()->input->getArray();
echo json_encode($data); exit;

Expected result

fileupload field data should be present

Actual result

fileupload field data is not present

System information (as much as possible)

Joomla 3.8.8

Additional comments

Files are uploading from the browser using multipart form
Files are appearing in the tmp folder
The _FILES global variable has the file information
No file information on Input object.

Workaround is to examine the _FILES global variable directly. The format is a little unusual due to the HTML array syntax of the upload parameters but it's parsable.