I'm experiencing this on Linux, with OOO300m7, Pavel Janik's build 9354. I can reproduce 
this, however I didn't do any further experiments. I'd rather have this working :).

So, if:
* I have a section with linked-to file, 
* and there are more than one footnotes in the linked-to file,
* and put cross-references (referencing the footnotes i the linked-to files) in the main file,
* and save the main file,
then:
* after the refreshing of the main file or after the re-reading it, the first of the cross-
references (referring to the 1st footnote) begins to show as referring to the 2nd footnote, 
and the 2nd cross-reference begins to show as "Error: reference source not found.". 

Double-clicking on the cross-ref in themain file yields then:
* in the 1st xref's Name field: 2nd footnote's name and text (read-only );
* in the 2nd xref's Name field: some read-only strangeness.

The main file's contents.xml show *seemingly* correct data, however (attaching the test 
case files).