If this happens on any journal screen, and you know things are setup correctly, most likely a user has entered two different values in the "Amount" and "Amount($)" fields.
Amount = Original customer currency
Amount($) = Your system base currency
If you enter two different values, an exchange rate is calculated and stored for that line.
You must delete the line and re-enter it, ensuring that you fill in the "Amount" field only, and allow the "Amount($)" field to populate automatically