Infinitely many finitely short time intervals cannot have passed after finite time, but infinitely many infinitesimally short time intervals can. In the same way that one way of conceiving infinity is to imagine it as an arbitrarily large value at any given expansion, but infinity in the limit, an infinitesimal is an arbitrarily small value at any given expansion, and zero in the limit.
That's the whole point. The atomic distance of a subdivided step goes to infinitesimal at the same rate that the time associated with the distance does, so we're fine!