They were warned

Prior to the JSF go-ahead, the General Accounting Office advised Congress to slow the program, arguing that, while good progress had been made in reducing technological risk, the program was still not a “low risk” venture. The GAO warned that cost overruns and schedule delays could loom in the future if certain of the program’s business, manufacturing, and weapons initiatives don’t pan out. The Pentagon rejected the assertion and insisted that the risks in JSF are well-understood and well within reason.

John A. Tirpak, A Strike Fighter,AIR FORCE Magazine / January 2002