The headline is spun. The text of the article doesn't allege "counterfeit titanium", only that the paperwork chain contains (according I guess to an audit done internally at Spirit) counterfeit documents. What that says about the metal itself is unknown. It seems more likely to me to be legitimate but stolen titanium than it does to be fake material.
It's not really feasible to fake something like a raw metal. Nothing else looks like titanium, nothing has the weight properties, even things like smells are different between metals that come out of different processes and tarnish in different ways. Basically by the time you got something that wouldn't be noticed by the assembly crews you'd have spent so much you might as well just have bought stolen titanium on the black market.