Clearly they changed something for this test in particular and it broke the system. It is likely something fairly minor that just doesn't work when part of it is removed.
Also, if it just went through a retrofit and has actually never fired a missile, then it's not unlikely for something to have been not quite placed back where it was supposed to be.
This is the difference between doing a release with a QA process that takes some time and testing versus doing development and just launching the new version into production.
They changed the code or hardware for this particular test. That not working does not prove that the system has fundamental flaws or that other systems that have been tested and not modified will have the same issue.
Most people do not understand the inherent brittleness in engineered systems. Even those that are designed to be fault tolerant. That can cause confusion about outcomes and the necessity of testing every release.