On the other hand, very brute numerics work for an awful lot of scenarios - that's why epsilon-delta came centuries after Calculus was invented.
For instance, "first-order optics" and "third-order optics" rise from chopping off the Taylor series after the 1st and 3rd term, resp. And it works! In many places, 1st order approximations are just good enough. A lot of scenarios are inherently stable.
So I don't think the intuition you build up is wrong - it just has a scope. There's nearly always a place for counter-examples where "things work the way you think they should" wouldn't apply, however you think about things :)
On a philosophical note, the continuity is a human construct - down there, things seem to be discrete, just with a very small step size. Continuity models these pretty well, until it doesn't - but that doesn't mean the intuition you build up is wrong. Just limited in scope.