I moved to the Isle of Dogs one week before the DLR opened, and have been using it ever since. Overruns are not normal (in most people's understanding of the term) but nor are they unknown.
When the system was brand new, using the single car stock that was long ago shipped to Germany, overruns happened in slippery conditions and I suspect the issue was crude anti lock braking system. One the current stock, overruns still do happen occasionally. If I guessed, I'd say I experience one or two per year, and are only a very small distance. The train captains are used to this and are slick at resetting the train and repositioning it (if needed - sometimes they appear to be able to open the doors if the train is only slightly off the correct mark).
My working career was not in railways but it did involve major change projects with massive software dependency. Project teams by their nature are short term entities and don't have the "collective memory" of what went wrong on previous projects. They also often have an "optimism bias". It is a failing of big projects the world over that too few managers are given the time and resources to properly study the issues that were encountered in previous deployment phases. And while I have no knowledge of the personnel leading this project, I have encountered many examples where the top man (and it usually is a man) makes it clear he doesn't want to hear bad news, so problems get concealed instead of solved. And then those problems blow up badly when they can't be concealed any longer.