The loading screen quote about turning off always run in battle was put in in the hope that players wouldn't discover how easy it is to dodge.
The Bruma Mages' Guild hall specializes in alchemy.The other six guild halls specialize in a specific type of spell. There are seven magic skills, six of which correspond to specific groups of spells. The reason that the people who sell spells in Bruma don't have one specific group of spell available is because they don't specialize in spellcasting. Instead, they specialize in making potions.
The hero was falsely imprisoned or framedThe hero specifically asked Uriel "Why am I in prison?" which gives the implication s/he did nothing wrong at all. Or more likely, Uriel being the seer that he seems to be, purposely (secretly) ordered the hero to be arrested and placed in that cell to fulfill the prophecy.
The Dark Brotherhood killed Count Indarys' wife.People in-universe and out always seem to blame the Count for his wife's mysterious death because he's apparently a scumbag. However, when you take into account the rumor that the Dark Brotherhood bribes said Count to keep his mouth shut about the existence of the Cheydenhal sanctuary (the exact words used are "bribes and other... incentives"), it could be possible that at one point he tried to do something about them, and they killed his wife to teach him a lesson. Because of his reputation, or maybe just because people are prejudiced against a dunmer Count, or even because of the Brotherhood themselves spreading rumors, everyone just blamed Indarys for his wife's death and decided not to look any further into it.
The Hero is into necrophilia.He or she knows the penalty for grave-robbing is death without being told beforehand and is able to rattle off the fine for necrophilia. Sounds like things someone would want to know if they were into dead bodies.