That sounds awfully strange. I have a hard time believing your 1099-DIV should have any figures that are fund-level, rather than shareholder-level. Can you piece together your dividends and cap gain distributions from your quarterly statements? Perhaps online distribution information? I've had to do that lately for interest paid that is under $10 for the year. Since interest rates are so low, it's not uncommon for total interest paid to be under $10, and no 1099-INT is generated as a result. You still have to report the number though. So I go through and just add it up from monthly statements. Perhaps you can figure out the right number that way.
If you're using a tax software package, you can see the effect of changing that one figure, right? That should give you a clue as to whether its backed out anywhere else. I rather doubt it is - I think you were given the wrong number. Can't imagine a fund-level figure ever would show up on an individual 1099-DIV.