My cat had an antibiotic injection about 2 hours ago, she has has just vomitted and it was brown, should I be worried?

Why don't you call the vet and ask them? ;)

Whether to be worried or not would depend on knowing what was the matter with him in the first place. Antibiotics by injection very rarely cause vomiting, So, best advice for an accurate answer is to call the vet back, tell him what is going on and ask him should you be worried.