I have field collection with only file fields. You can investigate - in this case $form won't contain #entity property which is necessary for altering it. So I've created small patch.
PASSED: [[SimpleTest]]: [MySQL] 132 pass(es). View
FAILED: [[SimpleTest]]: [MySQL] Unable to apply patch field_collection_0.patch. Unable to apply patch. See the log in the details link for more information. View