Well it appears Alpine has sent a new manifold with the holes slightly reamed out so the shop can more easily fit the injectors, which should be tighter than the stock fitment to prevent blowby. I've used Scotchbright, sandpaper or a dremel carefully on some that have been too tight - it is a difficult fit and knowledgeable mechanics should have no trouble. 3/100ths ain't that much...

Since the injectors should have been moved to the new manifold BEFORE installing the manifold on the engine, there would be no install charges to be responsible for - they should have stopped when they couldn't get the injectors to fit. The gaskets then would not have torqued down either although they are multi use gaskets.