I had an interesting job interview experience a while back. The question started really easy:
Q1: We have a bag containing numbers
Wait a minute. As the question is stated, there are 100 numbers in the bag. No matter how big k is, the problem can be solved in constant time because you can use a set and remove numbers from the set in at most 100 - k iterations of a loop. 100 is constant. The set of remaining numbers is your answer.
If we generalise the solution to the numbers from 1 to N, nothing changes except N is not a constant, so we are in O(N - k) = O(N) time. For instance, if we use a bit set, we set the bits to 1 in O(N) time, iterate through the numbers, setting the bits to 0 as we go (O(N-k) = O(N)) and then we have the answer.
It seems to me that the interviewer was asking you how to print out the contents of the final set in O(k) time rather than O(N) time. Clearly, with a bit set, you have to iterate through all N bits to determine whether you should print the number or not. However, if you change the way the set is implemented you can print out the numbers in k iterations. This is done by putting the numbers into an object to be stored in both a hash set and a doubly linked list. When you remove an object from the hash set, you also remove it from the list. The answers will be left in the list which is now of length k.