Oke, I was having this problem for the last three days. Now after a few hours after I posted this question I solved the problem.
For those who have the same question or problem here is what solved it for me and what the right way is to add settings. The settings can be different for each instance so the settings go at the instance creation and not the field itself.
Here is an example on how it is supposed to be:
$instance = array(
'field_name' => 'file'
'entity_type' => 'node',
'bundle' => 'article',
'label' => 'Attachment',
'description' => 'Add an attachment here',
'required' => TRUE,
'settings' => array(
'max_filesize' => '512',
'file_extensions' => 'zip txt pdf docx'
),
);
field_create_instance($instance);
The settings field is not required but i was using an foreach because I generate multiple fields and instances at once, if you do this and you have settings at 1 of your generated field instances then you have to add settings at all instances or check if it is there or not.
I hope my experience can help any of you out when having the same problem.