Broken Quests:

Randolf Safehouse 3 - No quest marker, I have cleared Fallon's department store several times... - Mission quest still asks me to clear the area of hostiles - Slept for several in-game weeks and it still says "Cleared" - What's the solution ?

Trouble Brewin' - Chose the option to keep "Drinkin' Buddy" myself and sent him to Spectacle Island - Nowhere to be seen - Mission still open with option to sell it to the guy at the Rexford Hotel - Where is the robot on the map ? - I don't want to sell it just to fix the quest.

Game bugs:

Night Person Perk - Night Vision still present when not sneaking, Have to bring pip boy up or press pause/unpause game to disable it. Uber bright with pip boy light on and crouched at same time, proper headache material.

General Query:

Where does Bethesda state that you "SHOULD NOT" explore the wasteland before jumping into the main quest line ? Because it seems that doing so breaks the game completely in mine and all of my friends cases.

Some clarity on what you can and can't do regarding locations needs to be conveyed by the company as i have a level 175 character that i use to hunt legendary weapons that it would appear won't be able to do the main quest line at all.

Simple Example:

Clear Hubris Comics of Ghouls is a quest given by settlers, How does one not stumble upon and then break the silver shroud quest by simply clearing the building and picking up the suit that's just sitting there ?

For the safehouse wait a few days, the enimies will respawn in a in-game month or so.

And for the Rexford hotel: also if you told him to go to a settlement he might be lost forever, it happens ALOT, they end up in a NPC room filled with other NPCs with no doors or actual location on the map.

If one finds the Silver Shroud costume first, it just adds a quest and points you to Kent in Goodneighbor.
That was how it played through the first time for me.

As to Trouble Brewing, that is not Broken.
Someone else made a post about sending folks to Spectacle Island and there is a good chance they were getting stuck in the odd terrain along the ocean floor on the way there.