Are you using a map when you search the census for your ancestor? If you don’t have appropriate, contemporary to your census problem year maps, you could easily be making mistakes or looking in places that are not quite right.
Do you know where all the lines are on the map of your ancestor’s neighborhood? Property lines, county lines, state lines, they all play a role in your family history research. These lines change over time as new territories are created, county lines are debated and finalized, and as your ancestor buys and sells property. Getting your ancestor’s maps all “lined” up may help solve your problem. And keep in mind that contemporary maps are always an excellent idea. Your ancestor probably did not live in the twenty-first century. Don’t rely completely on maps created a centry after he died.