When a formal system says: "this computation halts after some number of steps", then under the default interpretation that means that after say 10000 steps the computation really halts. But in the "similar but weirdly different" reality where transfinite numbers exist the above claim can still be considered true if it runs indefinitely. One simply has to entertain the idea that "some number of steps" might mean a transfinite number of steps.
In other words, yes, we can say that the formal system lies provided we accept that what is and what isn't a lie depends on the viewpoint.