Commands in UNIX are case-sensitive, you can't just capitalize random things. Also, awk is missing a quote.

Also, that can be simplified a lot...
1) awk does not need cat's help to read a file.
2) awk's separator defaults to space, -F" " is redundant.
3) grep can count all by itself, via -c.
4) You don't need ls and awk to loop through a directory.
5) You especially don't need to ls -l -t then just throw away everything -l -t does for you.

ls -r -l -t | awk '{ print $9 }' | ... simplifies to ls -r | ... See man ls to learn what these options do.

6) If test.txt already existed, you'd be adding to it instead of replacing it, ending up with more filenames than you expected. Use > instead of >> to overwrite.

7) You don't need a temporary file. You can pipe into a loop as easily as anything else -- in fact you do so already, but didn't join the two.

8) find is often better than ls -r. You can tell it to find only files, for example (which is what -type f means.)

9) You don't need to run grep 12 times for 12 files. It's quite capable of counting more than one file.

Since "echo a b c d e | xargs cat" is equivalent to "cat a b c d e", we can feed find's list of files into xargs grep to grep many files at once.

It will print lines like filename:2 which we can read directly, telling the shell to split on : (The -H forces grep to always print the filename)

10) You only check for two and exactly two matches. You'd miss a file which had three. Try -ge for "greater than or equal to".

Code:

find /path/to/folder -type f | xargs grep -Hc "not found" | while IFS=":" read FILE C
do
        [ "$C" -ge 2 ] && echo "$FILE contains 'not found' $C times"
done