Newbie

So this December we signed my wife up at the same gym I go to.
I was rather surprised how eager she is about it. (I`ve bought a few things
for her to exercise at home but she never really got 'into' it.)
Time is an issue since we spend a lot of wasted time in traffic and thus get to gym
late and even later home but were sticking with it.
I must admit it`s really nice having a gym partner again and one that helps
push to go (a gym memberships in South Africa is not cheap and some days self motivation is low)
So to get to the point:

She is really weak. She battles with most exercises. She`s never used her muscles before.
She battles since the smallest dumbbells are 2kg and most machines the first weight is 4.5kg, and it`s mostly
her shoulders. She says they click.
We gym together and she does everything with me, but at her own weight. This is the way she wants
to do it.
Also, a guy at work told her to avoid squat exercise because it will make her bum big.
This was the same guy that told her woman should ONLY use treadmill and bicycle so I doubt he`s talking sense.
She squats 10kg on a smith machine. Does his comment hold any ground ?
She cant do pushups and the barbells are all international BB and thus dry weight about 20kg...
The leg press machine weighs 75kg dry weight...
She has goals but would like to know how to go at it without injury, will the clicking go away if she
keeps training light (like with elastic bands etc.)
It appears she inherited it from her dad and almost all their joints do that.

We use bodyspace.bodybuilding.com to track all our workouts & body-stats since it has an excellent tracker,
but I doubt that info would be helpful...

Ps. Gotta say loved the "http://www.instaabs.com" 

Girl Box Squats 225 lbs @ 112 lbs body weight!

That man is wrong. :3  Squats does not equal big ass, unless you're on roids.

For the joints thing, consult a doctor because they're the experts.

As mentioned above, the big butt thing is complete tosh.

When encouraging women to take up some kind of resistance training I almost always here the same response: "eww, I don't want to have big muscles like a man" etc. etc. -- to which I respond, look around the gym at all the men lifting weights. A lot of them are lifting more than you ever will and are they big? On the whole, no. They're normal guys, but very very few of them are particularly big, and these are people who have a much better hormonal and physiological profile to build muscle than your average woman. So there is no harm in resistance training.

Your wife will not get a big bum from squats, however they will strengthen her immensely -- and not just her muscles, but much more to the point her connective tissue; ligaments, tendons and bones.

I would suggest getting her to work with her bodyweight 3x/a week or similar, but your routine is ofc up to you two as you are there and can see it and i'm just sitting at a screen using words. The clicking is almost certainly nothing to worry about so long as it is never painful. It sounds like it is an inherited trait and shouldn't be afraid of as a surprising proportion of the population has this to one degree or another (my wrists click when used at a certain angle, but it has never hampered my weight training or anything else). If you're unsure; consult your physician. However, I see no need to keep things light because of fear of the clicking; train as you'd want her to train as if it wasn't there.