I've bought this game the day it came out, and have played it every day for the last seven-plus months. And during that time, I've have played almost exclusively in Franchise mode with a few different teams and went through several seasons.
This morning, though, I noticed my first issue with it. I started a game and it was raining. Now I always change it to clear or partly cloudy, but clicked through too fast and forgot. By the third or fourth inning there was a rain delay.
Not a huge deal, right?
Well, one of my players hit a home run before the delay. It was his second of the season (it's still early April), and at the end of the game the box score did not listed his HR. It also didn't give any stats for my starting pitcher, and everyone on my roster had 2 at-bats.
Once I exited the game, it had my one player with only 1 HR, and my SP didn't have any stats because it was his first start of the season.
Not sure if it has something to do with rain delays, but I find it somewhat annoying.