(I am playing the game on the PS4 just for clarification)

I don't consider this a "game breaker" by any means but it's very annoying to me. In Sanctuary, I built a very large "home" and at the top of it I built a completely sealed room where I put the power armor and crafting stations and such. I thought the room would be safe from any NPC or invading marauders because I put a metal wall up everytime I left, effectively sealing off that top floor (or so I thought.)

Here's the point, I came back from a trip to Diamond City and removed the wall from the side of the top floor and there were like 3 NPC settlers just poking around in this supposedly sealed room. If characters can just enter any structure they want then what's the point in building shelters for them? I don't know why or how this occurs but it's pretty frequent and, unless I'm missing something, I didn't think NPC's could remove structures you've built for them. In my completely non-professional opinion, I think it's possibly linked to a clipping issue of some sort where NPC's are given free-reign of the settlement structures and these NPC privileges need to be revoked/patched/etc.
It would be understandable to see NPC's in the room if there was an entrance built into it but this particular room I sealed off intentionally and I really want my sealed rooms to remain sealed until I take the walls away.

One other thing about the settlers at Sanctuary (at least in my game). They are really rude! Why do you have settlers (who had NOTHING before you rebuilt the area by the way) who say things to the protagonist like "God, I hope you're not one of those Synths?" The dialogue these people have is just obtuse and definitely doesn't make the player want to help them out when they constantly gripe and moan about everything.

Anyway, please fix some of these things. Thanks guys. Love Bethesda!!

had an issue where my companion entered a sealed room as well.... and started fighting a ghoul... i was like ehhhhh???

That's not even close to what the OP is talking about. The room he's speaking of doesn't have any way to enter it, he's putting a 4th solid wall up.

Anyways, settlers from what I've read, (I believe it was even mentioned in one of the "tutorial" pop ups) that they can move certain things if they feel like they are in their way. I have actually had a turret or 2 moved on several occasions.

I was talking about a sealed room that was sealed way of Terminal as in the only way to get through to the room was the sealed door that was locked via a terminal. It happened at the National Guard Recruitment Armory. I thought it was a similar issue.

The room your speaking of has both a terminal and a door which are able to grant entry. And there are companions that can pick door locks as well as hack terminals so them doing so to get into the room is very likely possible to what happened to you. The OP was speaking of a room that had 0 doors, literally no possible way to get in at all, yet he was finding settlers inside.

So back to that, I still think it's a matter of the settlers moving junk. Maybe they moved your walls because they were like "What's this guy trying to hide from us?" it could just have been a pathing glitch too where they may have gotten stuck and just sorta popped in there.

No I see NCPs and mobs walk though walls/closed doors fly up on to roofs all the time. It seems like they try to get somewhere and the code helps them by porting them to where they want to go.

I get the impression this is a sloppy pre release hot fix to try and compensate for the abysmal pathfinding coding.

The only safe place to store items is in the workstation at your home in diamond city. For power armor remove the core. I'm not 100% certain these workarounds will always work but they seem to for me right now.

That's what I was tihnking it could've been some clipping issue because the walls never moved (unless they put the wall back after they entered the room). I returned to the sealed room, removed a wall so I could get into the room, and found NPC's inside.