A CT used for metering or protective relays should be sized for the FLA of the circuit. That being said, the difference you mention should not result in any significant damage from overheating. You didn't say if the CT was for metering or protection. If the CT is used for protection, relays commonly have tap settings above the rated 5A secondary current. If for analog metering, the meter is typically sized for the CT(250:5A CT, 250A max scale meter), and the meter may be damaged from over-scale readings.