Answering yes/no questions I was a bit surprised at first when I discovered that Chinese doesn't have single words or expressions for "yes" or "no", and that instead we must use the verb from the question to either confirm or deny. The difficulty is not insurmountable if we can understand the verb from the question, but there seems to be exceptions, and this brings me to the object of the question.

I have this sentence and I need to modify as a yes/no question and then answer both positively and negatively:


  Statement:
  我妹妹来美国。
  Wǒ mèimei lái Mĕiguó.
  
  Yes/No Question:
  你妹妹来美国吗？
  Nĭ mèimei lái Mĕiguó ma?


I answered with "来。／不来。", but looking at the key of the exercise, enough surprisingly I noticed I was wrong, since I should have answered "是。／不是。".

Why is 是 used here instead of 来？ Is this event contemplated in the grammar, I mean, are there rules/guidelines to know when we can use 是 even if it's not the verb used in the question?
Statement:
  我妹妹来美国。= My sister is coming to the States.
  Wǒ mèimei lái Mĕiguó.   
  
  Yes/No Question:
  你妹妹来美国吗？ = Is your sister coming to the States?
  Nĭ mèimei lái Mĕiguó ma?


Under this circumstances, both 来/不来 and 是/不是 are acceptable and can be understood with no difficulties. However, I have to disagree with your key to the exercise because 来/不来 is much more commonly used by native speaker. Chinese usually use the main verb in the questions to answer them. 

I can understand the confusion. It is probably caused by the fact that "是/不是" means the same thing for "yes/no", "is/is not", "are/ are not" and "am/ am not". Let me use a few example to illustrate my point:


你妹妹来美国吗？ Is your sister coming to the States?
The way Chinese commonly do is: 来。It means: Yes.


The full answer is: 是的，她来。Which, in English, should be:  Yes, she is. Here "is" refers to "is coming", where the main verb is"来".


你妹妹是美国人吗? Is your sister American? 
The correct way in Chinese is: 是的。Also means Yes. 


However, this time, the main verb is "is". So the full answer is "是的，她是的。"meaning, "Yes, she is." See we have two "是" here, meaning differently (yes and is) in English. This is where you need to use "是/不是”。