Steps to reproduce the bug:
1) Enable i18n in order to have a translatable content type (node_type_example)
2) Configure a field collection (field_data_field_collection) with a node reference field (field_data_field_collection_noderef)
3) Add this field collection to the content type
4) Create a new node, set it to "english" and add another node (english) as reference in the field collection node reference sub field (field_data_field_collection_noderef).
The language field in the entity field table (field_data_field_collection) is "en", instead the language field in the node reference sub field (field_data_field_collection_noderef) is "und".
5) The last step is to translate the node, for example in german.
At this point There are two errors:
Notice: Undefined index: nid in node_reference_field_prepare_translation() (line 883 of /var/www/sites/all/modules/references/node_reference/node_reference.module). Notice: Trying to get property of non-object in node_reference_field_prepare_translation() (line 887 of /var/www/sites/all/modules/references/node_reference/node_reference.module).
The field_data_field_collection table contains two records (it's what I'd expect), "en" and "de", but both have the same value which refers to the field_data_field_collection_noderef table which contains only the "und" record, shared between the translations.
Moreover there is a side effect: when you delete one of the two nodes the field_data_field_collection_noderef record is deleted. This will trigger more errors on the other node because field collections doesn't find any matching records.