"How many children do they have?"
吗 Ma is used for questions expecting either a positive/negative response; It is not used in other types of questions such as the "how many" here.
In this sentence the "?" symbol is the only thing we need to convert it in an interrogative sentence?
I guess you are asking whether the question 他们有几个孩子？is just made from the affirmative sentence 他们有几个孩子。by adding a question mark.
This way of making questions is also possible in Chinese, especially when we question with disbelief.
However incidentally this question is not. 几个 means How many, as well as Several. The affirmative sentence 他们有几个孩子。would usually mean he has several children. But 他们有几个孩子？would usually mean How many. It is not impossible that in some rare context it is questioning if they do have several children, just it is not very likely.
I used 她 and it marked it wrong saying I was supposed to put 他 Is there a reason for this or is this just the course doesn't have all the right answers still?
Maybe it's because you use 他 when there's even one male in the group, and I suppose this refers to one family/couple that has got children.
I was counted wrong for this same reason and marked that my answer should be accepted. Realistically 她们 could refer to a specific group of women, or sisters, or two women who are married.
It should be emphasized about the fact that Chinese language do not have a clear distinction to distinguish between 她 and 他. Since they cannot distinguish it, the answer refers into the more male-specific only and completely reject the fact that there are no differences except genders between 他们 and 她们.
Hmm... nowadays we DO distinguish genders in personal pronouns. Gender is an imported concept, but it is no more appropriate to use 他/他们 for both genders.
Here it is possible to use 她们 though as the subject can be a same sex couple or a group of female.
Which of 几 and 多少(duo shao) is used more? Or are they used in different situations?
Although there is no concept of countable and uncountable nouns in Chinese, words like these show a difference. 几 only works on something countable, whilst 多少 work on both. As Chinese has classifier, this difference vanishes as long as you can find the right classifier to go with 几.
How many hours is it by train?
坐火车要几小时？ XX 坐火车要几个小时？ √√.
坐火车要多少小时？ √√ 坐火车要多少个小时？ √√.
How much time is it by train?
坐火车要多少时间？ √√ 坐火车要几时间 XX？
What's the difference between 孩子 (háizi) and 小孩儿 (xiǎoháir) for child/children? Pimsleur uses the latter.
They are pretty much the same and interchangeable. 孩子 would be used even on teenagers, young men and young women when talking about children in the sense of son or daughter, especially someone's own one.
What is the difference between using 个几 and 多少 ? Tāmen yǒu jǐ ge háizi? 他们有几个孩子 Tāmen yǒu duō shǎo háizi？ 他们有多少孩子
It is not an acceptable usage. 们 is not a plural indicator and in Chinese we don't need a plural indicator. We add 们 only to refer to a group as a collective. We don't ask "how many 'collectives'". Compare this syntax with 他们有几个苹果？ then you will see it is not possible to add 们 to the noun here.
A sentence like this would make sense:
孩子们里面有几个男孩？/How many boys are there among the children?
"他们有几个孩子吗" would this still make sense instead of a question mark at the end?