First, make sure that the pivot calculation is set to what you want: if it's supposed to be SUM and it's set to MIN, that might explain it. Pivot tables are also unique in that they don't look at live data, they look at cached data (very useful for what-if scenarios). If the data that the pivot table was generated from was zero, and you changed the data, you need to refresh the pivot cache to reflect the new values (Pivot Table Tools > Options > Refresh).
Pivot tables also have a unique feature to inspect the underlying data and return only those values to a new sheet for when you don't know what's going on and want to see why: Just double click one of those "zeroes" and it will return the rows that created that data point.