Problems with the story of mass effect 2 and 3!

Ok this is about the Quarians and their flotila and home world. I want to know are they germiphobes or what? Because in the first mass effect Tali tells Shepard about how a atmosphere genorator was damaged and killed some of them.
So you would think they don't wear those biosuits on the flotila. You go to the Flotila on Mass Effect 2 and everyone has one on. Why did those others die? if all of the Quarians wear their biosuit even on there own ship then no one should have died.
Ok now lets go to Mass Effect 3 and the major problem I have with this is. You go to their homeworld and you can breath? WTF! You mean to tell me the whole time the Quarians were Lieing to everyone. Because they said that the Biosuits are to simulate their homeworld's envirorment. Which was not suppost to be oxigen. Hello am I the only one to see Shepard breathing on Tali's Homeworld?
Why would they need the suits if their homeworld was like earth and everyone's elses. I think this is a major problem with the whole story Tali and the rest of the Quarians are Germiphobic! They think they are getting sick but they can breath oxigen like Shepard. Because the Flotila and the Homeworld have it!