[Deadalready]

First off the car, I first collected all the parts a brought them back to Smitty
and buy the car then I immediately leave the Den however the next few
towns I never see the car anywhere then I notice a grey trunk section of
a car and tada, can acess it to put stuff in only thats all I get, the trunk
with the rest of the car not there like the trunks cut off. I can't even
acess the engine and whatnot but it still seems to speed map travel without
me having to refuel it. This may be related but it never got stolen in Reno
either.

The car is prone to dissappearing. As soon as I get the car, I drive it around den a bit before re-entering the map. It driving it around seems to help stop it from dissappearing unexpectedly, most of the time it helps to enter maps where you know the car will spawn easily (eg the first area of Vault City).

Personally as soon as I get the car I drive it around until I run out of fuel then leave it on map. What happens then is the car is left somewhere retrievable if needed, but the trunk follows my character around. The floating trunk is really useful for storing goods.

Next, I notice that I can't talk to bartenders if I have a non human in my party
such as Marcus or Skynet even if I have told them to wait or left them in a whole other town. This almost cost me the quest where you have to
find out who killed the whore in Redding.

This I have no idea about, maybe it's to do with your karma.

Next, I've seen this mentioned on the forums before about people attacking
for no reason, sometimes even when I put mine and my partys weapons
away they still attack, this has occured in Gecko with some of the glowing
ghouls, the captain of the guard in vault city and the gaurds in the NCR.

I tend to find if I want to go looting it's a good idea to save before hand. If someone even gives you a warning it's a good idea to load; I tend to find there are some very strange triggers to violent behaviour.

Sometimes I've searched chests and had people warn me about leaving their stuff along, then the next time I see them they immediately go ape on me. Vault City is an example of a city with zero tolerance to people even looking at their good once.

Gecko guys just attack for no apparent reason, I've had it happen lots of times. Load a save game if you get attacked and often nothing will happen the second time around.

Speaking of the NCR, there is annoying bit where trying to free the slaves,
I've killed all the slavers, but every time I try to access the consoles it say
I need to enter in the code, and no amount of science skill or explosives seem
to to anything...

They're odd machines, just keep clicking in them until the game gives a good luck roll and opens the cages. I don't think skill makes much of a difference but one can always return to the cages anyway.

Next a graphical error, occasionally the skill button will be replaced by a black
box and skills can only be accessed by holding down the left mouse button
on the object/preson you want to use the skill on or using a tool.

It's an indication that a nasty crash bug may manifest, I've heard it means there's too many objects in the game or something and merchants will stop supplying new goods.

I've had it happen uncountable times, the major begining trigger is opening the quest log and looking through it late in the game.

And last in the ending movies, if you have gone back to Vault 13 and watched
Harrigan slaughter everyone it says that you are the one who killed all the deathclaws, anyway around this?

I think its because without the Chosen's intervention Vault 13 would never have been discovered. Not fair though.