So I’ve added some mods to Fallout 4 but nothing much. I added the Unofficial Patch, Lowered Weapon, Power Armor Animation, Everyone’s Best Friend, CBBE, Bodyslide and Outfit Studio, and Lacy Lingerie. After doing a mission, I noticed that Dogmeat was completely transparent. He wasn’t totally invisible but like Predator cloaking. I didn’t mind and thought it was just a glitch but then I switched companions from Cait to Piper. Piper ended up doing the same thing. If I had her go into Power Armor, the Power Armor would cloak too. I tried all the steps, without removing the mods, to get them back but it didn’t work. I had to uninstall/disable all the mods then go through the process to disable character and then enable again. Walla! They are back from the ghost world! It also fixed a glitch with companion carrying weight, where if I took something I still couldn’t give anything to them, and Dogmeat not able to display his Heavy Dog Armor. I love mods and console commands!
My son had to completely remove the game and all mods and reinstall to get it back to normal after some bad mods. Thankfully his saves were on the could.
MysticHydro did you figure out which mod was the culprit?
What are you guys using to manage your mods? I use mod organizer, I love the way it uses virtual directories, and doesn’t actually touch your original directory, but some things aren’t compatible with that, and some stuff, you have to still put in manually.
I’ve tried to be very picky so far with what I install, until the GECK gets out of beta and things settle down a bit.
Polekatt I use Nexus Mod Manager. It makes it easy most of the time. Hardly ever have to manually install something.
Could be a texture incompatibility, I used to get them in Skyrim with glowing blue-purple cave interiors etc. Needed to reload the texture packs in the correct order if I remember correctly.
I used to use NMM but Polekatt put me onto Mod Organiser - a steep learning curve but I think worth it. NMM bugged out on me a couple of times that were quite annoying.
A recent official patch caused all dog armor except for light(?) to not appear on Dogmeat. This is a bug that Bethesda somehow caused. I noticed that companions would temporarily turn invisible upon entering stealth after that same patch as well. If the companion is staying invisible indefinitely, I’d have to agree that its a texture problem, likely stemming from CBBE.
Also ensure you use LOOT to keep your load order optimized.
Remember to refresh your ini files if you start having issues as well.
So many people up in here taking about mods. I love it!
Just started the game seriously. Already figured it out the game disables achievements even if I just want to use a better map. Unbelievable. Another problem is with the 60 fps lock which I managed to solve, but still, is it so hard to put it in the ingame option menu? And last, the texture bugs. OMG the texture bugs…if the game decides to load them properly 
buttstallion In order to renable achievements while using mods, a lot of people, including myself, use this mod with a decent success rate http://www.nexusmods.com/fallout4/mods/12465/?
buttstallion I had over 100 hours before i stopped playing it and never had that issue XD
yes, I also used that achievement mod to be able to get them.
And I never had those problems in your screenshots. shrug
Maybe because of the HD texture pack? IDK really, I don’t use any mods and this is a fresh install. And some area of the game is always looking like this 
buttstallion I had this issue to.
Install these mods:
“FAR optimizes and improves over 6000+ distant land textures, which means more performance and a more stutter
free experience. Other mods will just edit one or two textures, but I have gone the extra mile to pack in
as much detail as possible. For some reason, Bethesda made a big error when saving their distant land textures
and made them use twice as much memory as needed. This mod also fixes that while adding said extra detail.
Note: Nuka World and Far Harbor distant land textures don’t have any problems.”
- Vivid Fallout: http://www.nexusmods.com/fallout4/mods/25714/?
"Vivid Fallout is an overhaul of all landscape textures, but also trees, rocks, roads, bridges and some concrete stuff.
In many cases I just sharpened the games original textures somewhat, added new normal maps and a slight shadowing.
However, the result looks quite good and…
the textures are less V-Ram heavy than the original ones!"
These mods looks great and eat less Vram, better optimized. My game looks and runs better with them. After I installed these mods, the issue with textures aren’t loading disappeared.
P.S.: Official HD Texture Mod Sucks, uninstall it.
Deleted the official HD texture pack. No problem since then. But all NPCs is talking too fast, starting the next sentence before finishing the last one. Very annoying.
Stopped playing 10 hours after installing. So far no problems. XD
Managed to fix the dialogue, but you have to have v-sync on. Half of the problems can be fixed with the fps locked. Interesting.
But still, there are some funny and annoying bugs in the game Like this one I managed to record. Sarge, the robot in the walls.