If you are writing a manual or reference document, then you might want to include a cross-reference to refer the reader from one part of your document to another. Example: "For more information, see 'Field mice' on page 249." You can specify whether a cross-reference derives from a paragraph style, such as a heading style, or from a text anchor you created. You can also determine the cross-reference format, such as Page Number Only or Full Paragraph & Page Number.
The following are some known issues with the InDesign CS4 Cross-References functionality.
Issue: The Hyperlinks pane or Cross-References pane of the Hyperlinks panel may not appear if the horizontal line dividing them is moved to the very top or bottom of the panel. When in this state, double-clicking on either a hyperlink or a cross-reference will not bring up the Hyperlink Options or Cross-Reference Options dialog box as expected. 
Solution 1: Drag the horizontal separator bar from the topmost or bottommost position in the panel to expose both panes.
Solution 2: To modify the Hyperlink or Cross-Reference Options while in this state, select the hyperlink or cross-reference and choose the appropriate Options... command from the panel's fly out menu.
Issue: Cross-Reference name field is blank when the cross-reference is targeting an unnumbered paragraph and using only paragraph number as the cross-reference format. 
Solution 1: Use a cross-reference format that includes something other than the paragraph number.
Solution 2: Number the paragraph(s) via Type > Bulleted and Numbered Lists > Apply Numbers
Issue: When opening InDesign book composed of multi InDesign documents with one document in the book with missing plug-ins the following alert message: "<file_name.innd> uses one or more plug-ins that are not currently available on your system. Book operations will be disabled until you replace or delete this document, or install the missing plug-ins" is displayed for all other document in the book when updating all cross references from the book panel menu. 
Solution: Cancel the updating process, check the documents for missing plug-ins and resolve them, then open the InDesign book.
Issue: Pressing Ctrl+A to select all format definition in Cross-Reference Formats dialog box is not supported. 
Solution: Hold the shift key down while selecting the first item in the list, then the last item in the list.
Issue: When performing Relink Cross-Reference between two InDesign documents from the Cross-Reference palette menu and selecting the wrong file type (example .jpeg) the following error message is displayed: "Some hyperlinks couldn't be updated because the documents they point to are not open. Please open the documents or hold down Option/Alt while choosing Update Hyperlinks." 
Solution: Be sure to select correct file type for relinking.
Issue: InCopy stories that aren't checked out to an InDesign user aren't in the paragraph list for cross references in the New Cross-Reference dialog box. 
Solution: Change the assignment of the InCopy stories to the author of the cross-references for the time needed to make the cross-references.
Issue: After Edit > Undo of an action that deleted a cross-reference destination, the cross-reference still shows with the status Missing in the Hyperlinks panel. 
Solution 1: Save both documents and open the document with the cross-reference source(s).
Solution 2: Select the cross-reference in the Hyperlinks panel, choose Relink Cross-Reference... from the panel fly out menu, select the document with the cross-reference destinations, and click OK.
Issue: Page number listed as missing for a multiple document cross-reference when you copy/paste the text frame containing the cross-reference. 
Solution: Open the document with the cross-reference destination. Double-click on the cross-reference to bring up the Cross-Reference Options dialog box. Choose the document that contains the destination and reselect the destination paragraph.
Issue: When no documents are open, the Define Cross-Reference Formats menu option is disable from Hyperlinks fly out menu. Application-wide defaults are not supported for cross-reference formats. 
Solution: Define default cross-reference formats as part of your document template(s). These can then be loaded via the Load Cross-Reference Formats... command from the Hyperlinks panel's fly out menu.
Issue: New Cross-Reference or Hyperlink dialog remembers any modified values if canceled. 
Solution: Reset to your preferred values before canceling, or when you next create a new cross-reference or hyperlink.
Issue: The paragraph styles list in a New Cross-Reference dialog box is showing styles that are not used in the selected document. 
Solution: None available at this time. Check regularly for available updates.
Issue: Deleting cross-reference destinations that are part of tagged text frames causes the cross-reference to display Overset Text status rather than Missing. The Got to Destination command is still available, though it does nothing. 
Solution: Untag the text frame(s) before deleting.