Set entity reference target_id in migration yml
Old question, but I'm guessing you need to add the array for the item list. I was successful with:

field_something/0/target_id: YOUR_VALUE_HERE


I haven't found documentation on the slash in the field id, but it is an array notation. The above is equivalent to something like:

$destination_values['field_something'][0]['target_id'] = YOUR_VALUE_HERE