CakePHP 3.5 checkbox array

First of all, you HTML has some problems. The form cannot be a child of the table so wrap the table by form.

As you can read the documentation it says

'hiddenField' - For checkboxes and radio buttons, by default, a hidden input element is also created, along with the main element, so that the key in $this->request->getData() will exist even without a value specified. For checkboxes its value defaults to 0 and for radio buttons to ''.

So if you inspect your code you will see something like this

<input type="hidden" name="Question[id][]" value="0">
<input type="checkbox" name="Question[id][]" value="2">

That's why you are getting some 0 values as well.

This can be disabled by setting 'hiddenField' to false:

<?= $this->Form->checkbox('id[].', array(
    'value' => $question['id'], 
    'name' => 'Question[id][]', 
    'checked' => false, 
    'hiddenField' => false
)) ?>

So the final code will look like this

<?php

/**
 * @var \App\View\AppView $this
 * @var \App\Model\Entity\Question[]|\Cake\Collection\CollectionInterface
$questions
 */

use Cake\ORM\TableRegistry;

?>
<nav class="large-3 medium-4 columns" id="actions-sidebar">
    <ul class="side-nav">
        <li class="heading"><?= __('Actions') ?></li>
        <li><?= $this->Html->link(__('Courses'), ['controller' => 'Courses',
                'action' => 'index']) ?></li>
    </ul>
</nav>
</nav>
<div class="questions form large-9 medium-8 columns content">
    <fieldset>
        <legend><?= __('Add Question') ?></legend>
        <?= $this->Form->create($question) ?>
        <table cellpadding="0" cellspacing="0">
            <thead>
            <tr>
                <th scope="col"><?= $this->Paginator->sort('checked') ?></th>
                <th scope="col"><?= $this->Paginator->sort('id') ?></th>
                <th scope="col"><?= $this->Paginator->sort('question') ?></th>
                <th scope="col"><?= $this->Paginator->sort('marks') ?></th>
            </tr>
            </thead>
            <tbody>
            <?php foreach ($questions as $question): ?>
                <tr>
                    <td><?= $this->Form->checkbox('id[].', [
                            'value' => $question['id'],
                            'name' => 'Question[id][]',
                            'checked' => false
                        ]) ?></td>
                    <td><?= $this->Number->format($question->id) ?></td>
                    <td><?= h($question->question) ?></td>
                    <td><?= $this->Number->format($question->marks) ?></td>
                </tr>
            <?php endforeach; ?>
            </tbody>
        </table>
        <?= $this->Form->submit('Save') ?>
        <?= $this->Form->end() ?>
        <div class="paginator">
            <ul class="pagination">
                <?= $this->Paginator->first('<< ' . __('first')) ?>
                <?= $this->Paginator->prev('< ' . __('previous')) ?>
                <?= $this->Paginator->numbers() ?>
                <?= $this->Paginator->next(__('next') . ' >') ?>
                <?= $this->Paginator->last(__('last') . ' >>') ?>
            </ul>
            <p><?= $this->Paginator->counter(['format' => __('Page {{page}} of {{pages}}, showing {{current}} record(s) out of {{count}} total')]) ?></p>
            <?php //$this->Form->button(__('Submit'), ['action' => 'existingQuestion'])
            // $this->Form->submit('Save');
            // $this->Form->end() ?>
        </div>
    </fieldset>
</div>