Cross references to table footnotes are not going to the correct paragraph
If you create a footnote, and then you try to create a cross-reference in another paragraph to the same footnote, the links in your output will not point to the correct location. Since FrameMaker stores the footnote details as part of the originating paragraph, the cross-reference to that footnote will end up pointing to the original paragraph for which the note was created.
This behavior is the result of a bug in the ePublisher application; we're not processing the footnotes quite right. We are aware of the isue; for your reference, the defect number in their tracking system is WWEP2467. A timeline for the fix is not yet available, but it will be listed in the Release Notes of the version for which it is addressed.
The only workaround I can think of is to create your footnotes manually. Add the appropriate paragraphs below the table, and then insert cross-references (or hypertext) in the table cells that should link to those notes.