How to fix ..?

By city wise report, are you referring to the Geosegmentation Cities report offered out of the box?

That report is based on a lookup table, which is actively maintained. It would be highly unlikely for a default report to have the same line item multiple times, unless they were genuinely different cities.

If it's a custom report (such as based on an eVar), then you would want to double check the values and make sure they are indeed passed into Adobe Analytics the same.

If you can provide more details on the exact report you're looking at, the date range, etc, we might be able to help further. Since this issue also may appear to be specific to your organization, it may also be a good idea to consider opening an incident with Customer Care.