Most solicitors will draw a clear distinction between fees and outlays. Outlay is money the solicitor has to spend on your behalf, and is always charged on an "as incurred" basis. Land Registry fees fall into this category.
It may help to give you some perspective if I say that if the solicitor had mistakenly taken €250.00 too much in respect of outlay, he would have to refund it to you. If he didn't and it was seen on a Law Society Audit, he would get a firm rap on the knuckles.
So, while you are right to be mildly irritated, I think you should pay up.