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.

Files: 
CommentFileSizeAuthor
#3 field_collection.patch513 bytesGeorgique
PASSED: [[SimpleTest]]: [MySQL] 132 pass(es).
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field_collection.patch689 bytesGeorgique
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.
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Comments

Version:7.x-1.0-beta5» 7.x-1.x-dev
Status:Active» Needs review

My patch is generated by PhpStorm, not sure it will pass check but let's try...

Status:Needs review» Needs work

The last submitted patch, field_collection.patch, failed testing.

Status:Needs work» Needs review
StatusFileSize
new513 bytes
PASSED: [[SimpleTest]]: [MySQL] 132 pass(es).
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Removing my local garbage from the patch