The two is always missing because on the first iteration of your loop you overwrite it with the call to strcat.
After entry to the loop your buffer contains: "1\02\03/4/5/6" internal strtok pointer is pointing to "3". tokens[1] points to "2".
You then call strcat: "12\0\03/4/5/6" so your token[i] pointer is pointing to "\0". The first print prints nothing.
Subsequent calls are OK because the null characters do not overwrite the input data.
To fix it you should build up your output string into a second buffer, not the one you are parsing.
A working(?) version:
#include <stdio.h>
#include <string.h>
int main(void)
{
int i = 0;
char *token[128];
char tmp[128];
char removed[128] = {0};
strcpy(tmp, "1/2/3/4/5/6");
token[i] = strtok(tmp, "/");
strcat(removed, token[i]);
printf("%s\n", token[i]);
i++;
while ((token[i] = strtok(NULL, "/")) != NULL) {
strcat(removed, token[i]);
printf("%s", token[i]);
i++;
}
return (0);
}