First of all make sure that you are not reading newlines and carriage return symbols. Input can be read like:

    char c;
    int scanfRez;
    do {
        scanfRez = scanf("%c", &c);
        if (scanfRez != EOF && c != '\n' && c != '\r') {
            chs[chCount++] = c;
        }
    }while(scanfRez != EOF);

I was getting WA7 with this input reading:

    char c;
    int scanfRez;
    do {
        scanfRez = scanf("%c", &c);
        if (c != '\n' && c != '\r') {
            chs[chCount++] = c;
        }
    }while(scanfRez != EOF);

If you get WA3 make sure that you are processing sequence correctly with given sequence length > N. For example:
let N = 11, input sequence = "abcdefghijkl" (without quotes) then letters should be removed in this order:
k 1
j 2
l 3
b 4
e 5
i 6
g 7
h 8
d 9
a 10
c 11
f 12

It does not matter if you put newline at the end of output.