The answer really depends on the house. If all the bedrooms are of a good size in a three bedroom house then yes the three bedroom house is of more value than a two bedroom house. But if all the bedrooms are small (in a three bedroom house) then it could be worth less than a two bedroom house as it makes more sense to remove some walls to convert into more practical bedroom space that is more useable than try to fit into something that is too small.
Most likely it is due to the asking price being too high. Try to price the property based on what comparable property is selling for in the area and make some adjustments for size or condition. Never make the mistake of trying to price a property on what it would sell for to the one dream buyer from Auckland as it never happens! BE REALISTIC! Don’t be scared to ask for buyer feedback from your agent.
Sometimes a bank will request a valuation to satisfy there lending requirements. Don’t worry as it is and has been standard practice for some time and is there for ‘checks and balance’ in the industry. It is good for buyers peace of mind as well to make sure the price they are paying is what it is worth.