I have tried to scan my Mellel docuement trough Bookends and it finds a bunch of ambiguous citations but the the text doesn't makes sense which makes me confused what to do.
Bookends is just displaying what Mellel sends it, so I'm guessing the problem is on the Mellel end. I'd see if a fresh document gives the same problem. If not, the document might be damaged in some way (I can't say), in which case I'd contact Mellel tech support. If the same thing happens with another document I'd try reinstalling Mellel (the latest version).