There's always stuff to do with new houses, so just because an engineer spotted it, doesn't necessarily diminish the value of the house, I would think.
It's really down to how big a deal this house is to you. Ask for the full amount if you are prepared to walk. I wouldn't think there's a 'right' or 'wrong' position in this, strictly speaking. It's more a negotiation tactic. I personally think that negotiating at the final contract stage is too late.
On balance, I'd say splitting the costs isn't a bad deal, as both parties have already sunk time and costs in to this transaction, and it's in both your interests to wrap it up and move on.