No Mutants Allowed

Perhaps it has something to do with the number of mods I have put on it, or the remains of mods that I did not completely remove previous (meshes, textures, and such).
Or the number of saves? I honestly don't know.

One of the issues is that enemies for example spawn on places where they should not be.

Did you use any particular mod manager? Like FOMM or NMM, for instance.

I am using FOMM and NVSE script extender, could that be causes?

Edit: Something else the game also starts to suffer from is that NPCs pathfinding routines sometimes simply don't work any more.
In one case it prevented an ingame cutscene from running, preventing me from continuing.

Welp, it could be anything from what you described. Could've been load order, could've been 2 different mods having conflict with one another.

I suggest switch to Mod Organizer if you're not that far into playing the game. With MO, the mods were stored into a different virtual directory, it literally didn't touch NV root folder.

I have made some progress in the game but I could always start over again.
First time BTW that I hear of that program, Mod Organizer.

Well damn, man. Mod Organizer has been around for some time, and honestly the best go-to mod manager for Beth's engine-made games. Since, like I said, it literally didn't touch your game's folder because it install all the mods into a virtual directory.

It requires a bit of learning and setup, tho. I suggest Fear&Loathing in New Vegas guide.

It's the amazing Power of bethesda's version of Gamebryo.

I am going to have a look at that program later, after reading your post I looked up the page where I can download it.

And yeah it is also the engine. Weird thing is that everything starts pretty stable the first couple of times you play new sessions on it, but then errors start to creep in the longer you run the program.

Uhm some time I get this when working on my mod like funny glitches that really should happned. Like with packages and pathing issues. But starting a new game and redownloadig mods should fix it

I have indeed un-installed FNV and deleted the data map to make sure that the remains of mods that I tried to remove and then reinstalling the game and mods all over again.
However I am using a save game from before I reinstalled the game, could that still cause some of the problems such as NPCs spawning on the wrong place or have pathfinding problems?

If there's a problem with NPC scripting, it's something wrong with your save, likely caused by your mods. Skyrim had that same problem.

What is the best way to solve NPCs issues that may be related to mods and saves Ben?