Why does competing the game fail certain missions?

Oh... you didn't finish Human Error. Do yourself a favor, do not get it spoiled for you. In my opinion it was the best questline in the game. I'm not sure why it failed, but if the institute was destroyed... it kind of makes sense.

But back to Human Error. It is the only F4 quest that presented me with an actual moral quandary. I went with Minutemen on my first playthrough. The only unambiguous "good guys" in the game. And I found and set out on Human Error pretty early on. And given I didn't really know much about the whole commonwealth lore so far, trying to determine who was right and wrong was... difficult. In the end I sided with the side I thought was morally wrong, just to avoid doing something a: really difficult for my level and b: out of character and pretty morally bankrupt.

It was hard to live with the choice I made in that quest. Well, relatively for a video game anyway. If you didn't spoil it for yourself, make sure you get to level 10 or so and then go to Covenant and try it for yourself. It's a good one. The reason I suggest this for a second or newer started character is... anything near or over level 20 or so would be waaaayyyy overlevel for this. Turning any fights... into just a series of executions. However, I was underleveled and it affected my decision.

"Who built this f#(%!^g police station." -- Leon Kennedy

I failed the Virgil quest on accident. Forgot to get that mutant his serum and he went ape spit on me when I visited him later. Oops. I think I'll play it again from the point where I discover the institute.