We are currently building a house, however have just discovered…

Hi and welcome.
That seems to be an extraordinary difference in what you wanted and what the architect designed. It seems to me to be a fundamental mistake. Hopefully another architect can assist with a redesign so that you get what you wanted rather than this mistake.
The 1st step should be a serious discussion with the architect, about this most recent serious issue, but perhaps with the other mistakes raised. He/she must explain what has happened and the effect and implications on the cost. It seems extraordinary to me that if you asked for a 340 m² property that he designed one at 470 m², and it is obvious that the additional cost would be well beyond your present figures.
So this discussion with the architect will be critical as to whether you continue using his/her services. The explanation which was given will be important deciding if there is enough basic competence.
At the same time, you may want to get an opinion from a senior architect so that you can approach your existing architect with a more informed knowledge of what has happened and the appropriate remedy. Obviously the quantity surveyor will be important as well, because the costing issues need to be raised with the present architect as well, and if you can show the architect that the costs have ballooned with the quantity surveyor information, that will give him/her some difficult questions to answer.
An architect like any other professional, owes a duty of care to his/her customers. This means that if he/she was negligent in her/his work, and this negligence causes losses, then they are liable for the losses. So the cost of a redesign to fit within your expected size and the delay costs in filing amended material through the Council, are matters where he will be liable