Following Charles' recommendation would mean starting again so you might not want to do that, however if every one of your xrefs is pointing at the wrong thing you will have to do that anyway. A caption-based numbering solution would be more typical and it depends on how you want the Equations to look as to whether that suits you better (eg. do you want the caption # on the same line as the equation or below/above)

In order to work out what is going wrong, you need to reveal field codes on the xref and see what bookmark it is pointing at. You then go to the location of that bookmark to see what it includes.

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Andrew Lockton
Chrysalis Design, Melbourne Australia