Both fares are SDR and set by ATW, so no obvious reason.
It's even cheaper (£9.70) from Earlestown to Shotton if you go via Liverpool.
It's cheaper again if you go via Liverpool and split at Bidston (7.90 single, 9.70 return). If you want a direct train, splitting at Helsby brings the price to Frodsham down to £9.90 single, £10.60 return.
It's all down to clusters, of course. Shotton-Frodsham costs as much as Flint-Irlam, whereas Shotton-Earlestown is the same as Upton-Prescot. No-one cares enough to check that the individual journey costs are reasonable.
That isn't the reason why Wrexham General-Helsby costs £4.20 single, £5.60 return whereas Wrexham
Central-Helsby costs 10p less each way.