Playing as Desportivo Brasil (starts Série G, Paulista Série B/Paulista 4th Division), I'm having a similar issue to one described earlier in the thread in that there is some kind of issue with the SP State Championships. First season, I won the 4th Division and was promoted from Série G to Série F, but the next season I only had Série F fixtures, none for the SP State 3rd Division. That competition showed as "This competition has yet to be scheduled" even when all the other state championships had been, and as I've kept playing (being promoted successively up to my current season in the Série D) the SP State 2nd Division has also stopped being scheduled, and so now in my current season there are only 8 teams in the Paulista State Championship (First Division), as 4 teams have been relegated and none replace them. The other problem that I noted with it was when the initial thing happened that I wasn't in the SP State 3rd Division, I looked at the other SP State divisions, and found that the SP State Fourth Division was split between teams from SP State, and teams not from SP State (for example, ones from Bahia, Distrito Federal, etc).
The one other (much more minor) quibble that I have is that the reputations for teams starting in the fictional Séries can get out of whack with reality: in 2014, I'm in the Série D with a "Worldwide" reputation along with Ituano and Vera Cruz-PE, and 15 other clubs have "Continental" reputations. The Série C similarly has Botafogo-SP with a Worldwide reputation, even though none of the teams in the Série A have such a reputation (15/20 teams in the Série A have Continental reputations, the balance National).