The main issue in your script seems to be that i takes the actual file names as values, while j is just a number. Taking the names to an array and using both i and j as indices should work:
files=(*)
count=${#files[@]}
for (( i=0 ; i < count ;i++ )); do
for (( j=i+1 ; j < count ; j++ )); do
if diff -q "${files[i]}" "${files[j]}" >/dev/null ; then
echo "${files[i]} and ${files[j]} are the same"
fi
done
done
(Seems to work with Bash and the ksh/ksh93 Debian has.)
The assignment a=(this that) would initialize the array a with the two elements this and that (with indices 0 and 1). Wordsplitting and globbing works as usual, so files=(*) initializes files with the names of all files in the current directory (except dotfiles). "${files[@]}" would expand to all elements of the array, and the hash sign asks for a length, so ${#files[@]} is the number of elements in the array. (Note that ${files} would be the first element of the array, and ${#files} is the length of the first element, not the array!)
for i in `/folder/*`
The backticks here are surely a typo? You'd be running the first file as a command and giving the rest as arguments to it.