How do I fix that in C?

In order to do what you want you should not read the values via fscan's %d format, but just tokenize the string, i.e. subdivide it into strings. You can do that with fscan's %s format, although I would prefer other means. So your loop could look like:

// improved code, but not really good; see below
char str[100];
int value;

while (fscanf (fp, "%s", &str) == 1)         
{
    if (sscanf (str, "%d", &value) == 1)
        i++;
    else
        printf ("Input <%s> is not a number", str);
}

There are two reasons, why I don't like the scanf functions: For one they offer no control over handling newlines. A newline is just another whitespace character. So if your input would be

5
12 56 89
34 52

it would be regarded as legal input. The second reason is that is inherently unsafe, as you cannot specify the length of your input buffer for the %s format (I put in 100 in the example above).

As an alternative to scanf I would prefer to first read the input line by line with fgets. Then parse the line by strtok, and finally convert it to integers by strtol.

#include "stdafx.h"

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>


char  *fname ="E:\\00-C++\\VC2010\\PROJEKTE\\testfile.txt"; //filepath with the numbers
const int   first_min       =3;  //min number count for line 2
const int   first_max       =12; //max number count for line 2
      int   first_number    =0;
const long  second_min      =100;
const long  second_max      =1000000;

const int   max_linelength  =100;  // make sure that real file-line-length is shorter than max_linelength
      char  line[max_linelength+5];
      int   lineno          =0;

      long  number[first_max+5];
      int   ixnumber        =0;

//--------------------------------------------------------------------------------
void funcPrintRuler()
{
  printf("\n");
  printf("\n.........1.........2.........3.........4.........5.........6.........7.........8.........9");
  printf("\n123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890");
}

//--------------------------------------------------------------------------------
int funcOnlyDigitsOrSpaceAllowed(int lineno,char *line)
{
  int   kzdigit =0;
  int   pos     =0;
  char  *p      =line;

  while (NULL!=*p)
  {
    pos++;
    if (isdigit(*p))  {kzdigit=1;p++;continue;}
    if (' '==*p)      {p++;continue; }

    funcPrintRuler();
    printf("\n%s",line);
    printf("\n%d.line: Only digits or space allowed. pos=%d",lineno,pos);
    printf("\n");
    return 0;
  }

  if (0==kzdigit)
  {
    funcPrintRuler();
    printf("\n%s",line);
    printf("\n%d.line: digits are missing",lineno);
    printf("\n");
    return 0;
  }
  return 1;
}

//--------------------------------------------------------------------------------
void funcGetNumbers(int lineno,char *line)
{
  char  *p  =line;
  ixnumber  =0;

  while (NULL!=*p )
  {
    if (ixnumber>=first_max) return ; // too many numbers
    if (' '==*p) {p++; continue;}

    number[ixnumber]=atol(p);
    while( NULL!=*p && isdigit(*p))  {p++; continue;} // goto next number
    ixnumber++;
    p++;
  }
}

//--------------------------------------------------------------------------------
int funcCheckLine1(int lineno,char *line)
{
  funcGetNumbers(lineno,line);
  if (1!=ixnumber )
  {
    printf("\n%d.line=%s<",lineno,line);
    printf("\nonly one number allowed");
    return 0;
  };

  if ( number[0]<first_min || number[0]>first_max )
  {
    printf("\n%d.line=%s<",lineno,line);
    printf("\n%d.line contains number=%d,  but must be >=%d and <=%d",lineno,number[0],first_min,first_max);
    return 0;
  }
  return 1;
}

//--------------------------------------------------------------------------------
int funcCheckLine2(int lineno,char *line)
{
  int i;
  funcGetNumbers(lineno,line);
  if (ixnumber!=first_number )
  {
    printf("\n%d.line=%s<",lineno,line);
    printf("\nnumber count=%d, but must be %d",ixnumber, first_number);
    return 0;
  };
  for(i=0; i<ixnumber;i++)
  {
    if (number[i]<second_min || number[i]>second_max )
    {
      printf("\n%d.line=%s<",lineno,line);
      printf("\nnumber %d=%d, but must be >=%d and <=%d",i+1,number[i],second_min,second_max);
      return 0;
    }
  }
  return 1;
}

//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
//--------------------------------------------------------------------------------
int main(int argc, char *argv[])
{
  int   i;
  FILE  *fp;
  int   lg=0;

  printf("START");
  
  fp = fopen (fname, "r");
  if (fp == NULL) { printf ("Cannot open: \n%s",fname); goto w_err;}

  while (NULL != fgets(line, max_linelength, fp))
  {
    lineno++;
    lg=strlen(line);
    line[lg-1]='\0'; // remove '\n', only for printf line, not nessessary for read numbers
    //printf("\n%d. line=%s<",lineno,line);

    switch( lineno )
    {
      case 1:
        if ( !funcOnlyDigitsOrSpaceAllowed(lineno,line) ) goto w_err;
        if ( !funcCheckLine1(lineno,line) )               goto w_err;
        first_number=number[0];
      break;
      case 2:
        if ( !funcOnlyDigitsOrSpaceAllowed(lineno,line) ) goto w_err;
        if ( !funcCheckLine2(lineno,line) )               goto w_err;
      break;
      default:
        // do something
        printf("\n%d.line=%s<",lineno,line);
    }
  }
  fclose (fp);


w_ok:
  printf("\n\nFile Content:");
  printf("\nline 1 read %d=number count for line 2",first_number);
  for (i=0; i<ixnumber; i++)
  {
    printf("\nline 2 read %d.number=%ld",i+1,number[i]);
  }
  printf("\nprogram OK");

  getc(stdin); // only pause
  exit(EXIT_SUCCESS);

w_err:
  printf("\nprogram error");
  getc(stdin);
  exit(EXIT_FAILURE);
}