I believe they had to change the landing site for some reason, and the simulations they ran were for the initial landing site, where a 3KM crater would not have been encountered.
The Eagle ended up off course, but I've seen multiple reasons given. One is that they modelled the moon as perfectly round, which turned out to be incorrect, mucking up timing plans. The side facing Earth is more dense, due in part to being tidally locked I believe.
The control room was sweating when the landing deadline passed beyond the expected margin of error and they were still flying.
Lesson: always leave a margin of error, especially on the first mission. Armstrong's calmness and clear thinking under duress paid off.
