there are two things that I know of that will cause a companion to go missing that aren't bugs.

1.) check to make sure you companion is set to 'follow' and not 'wait here' before fast traveling. There might be conditions that will set your companion to 'wait here' without your knowing it. Remember that there are certain areas (like the casinos) where you character cannot follow. When you enter such a place, your companions is automatically set to "wait here."

2.) when you are moving through broken terrain, and especially when you are doing jumps and otherwise forcing a difficult crossing, always look behind you and see if your companion can follow. I've noticed that companions can duplicate some feats of movement, but not others. When a companion cannot get to where you are the way you got there, it will try an alternate route, which (given the broken terrain) may take it on a long and winding route away from you. This is how some companions 'just vanish' and then end up being killed somewhere by themselves. So if you see you are going to cross some rough terrain, do a save first in case you companions ends up running all over the place.

3.) This one I'm not sure about but it worth looking into. Watch out for area that are within areas. I.e., the Strip is inside Freeside, which is inside the Mojave. If you are inside of something that's inside of something, you may have to go completely to the original outside again for your fast travel to take your companion with you. At each stage of getting outside, check that you companion is still set to 'follow.'

Helpfull stuff, Im like a paranoid courier atm, every two steps I look at teh back to see if they are still there lol. :intergalactic:

I'll add a two more things I noticed.

1.) I said before that you should always look behind you when you cross rough terrain to see if your companion can do what you did to cross it. Now I'll add that even relatively clear terrain can be a problem for a companion too. Sometimes they can get stuck behind a sign or a piece of fence or whatever and continue running in place but not getting any where. You then have to move at a diagonal to them to make them go around the obstacle. So when moving with a companion, always move a little bit and look behind and repeat.

2.) When you get into Freeside or the Strip, there are hired guns waiting for you at the gate. You can hire them in addition to your companion to escort you through Freesde or the Strip. They help you take care of pickpockets and random thugs. (especially in Freeside). But I have had one instance of hiring one in addition to my companion, and then finding him gone after I exited a casino - while my companion was still there. I don't know if this is a bug or if its just a con these kinds of hired guns are running.