The final two episodes of Neon Genesis Evangelion are pretty notorious; those two episodes may be the most notable examples of "Man,that was going distinguished but they really whiffed the ending" in anime history. In fact, they were so controversial that the show's creator, and Hideaki Anno,and the studio, Gainax, and actually released two films,Death & Rebirth and End of Evangelion to kind of "replace" the ending.
Source: blastr.com