Your error is in these lines:
for (var i = 0; i < numbers.Length; i++)
{
numbers[i] = input;
count++;
}
You are initially assigning the input to all array elements overwriting all values entered previously.
Think about the requirement. It is not difficult (based on your code):
while (count < 5)
{
var input = Convert.ToInt32(Console.ReadLine());
bool duplicate = CheckDuplicate(input, numbers, count);
if (duplicate)
{
Console.WriteLine("Duplicate entry. Try again.");
}
else
{
numbers[count] = input;
count++;
}
}
All you have to do is writing a function that checks for a duplicate (or replace the function call by code doing the same). The check requires three variables: the input value, the array, and the number of values added so far.