From my recollection, player progression and weekly prep weren't
broken per se, but they were obtuse to use.
Weekly prep being obtuse is obvious. Setting up the schedule of activities was a chore akin to setting up a Microsoft Excel document, and configuring it in such a way where the list of activities would result in a net positive benefit for your team was extremely challenging in the worst possible way. There was little to no prior guidance or after-the-fact feedback as to why certain results from weekly prep occurred given the list of activities one passed in. It was a mechanic which suffered greatly from poor communication and poor user interface, and while well intentioned it was probably too smart and too detailed for its own good. It was not engaging to use and it didn't intelligently reward the user for experimenting with it. I remember a lot of passing around of weekly prep set-and-forget templates on this forum back in the day.
Player progression was similarly obtuse at best (possibly influenced by weekly prep? it was unclear) and predetermined at worst. My personal experience with this was having a second-year quarterback make the Pro Bowl and win Super Bowl MVP only to regress below OVR 70 entering his third year. Regardless whether such a flash-in-the-pan career arc is realistic or "sim", it was quite simply frustrating as a person playing a video game to watch the game outright punish my achieving successful results. That lone memorable outcome soured me on the game's franchise mode entirely and I never touched it after that.
The more memorable bugs and issues in NFL 2K5's franchise mode centered around CPU team management AI, specifically trade logic and draft logic. CPU teams only took very specific positions with first-round picks, and the trade logic was aggressively fuzzy at best. Additionally, in a couch multiplayer setting, games could only be played in the order they appeared on the schedule, which in that specific gaming setting was a crippling shortcoming compared to Madden 2005's play-the-weekly-games-in-any-order flexibility.