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Since the awk body is in single quotes, awk does not see the shell variable. awk thinks you mean an awk variable i. That variable is undefined, so in a numeric context it has the value zero. Thus $i is interpreted by awk as $0, or the whole line.

You need to pass the shell variable into awk.

for ((i=1; i<=$count; i++))
do
    abc=$(awk -F "," -v col=$i 'NR==1 {print $col}' $file)
    #................^^^^^^^^^...............^^^^
    echo "$abc"
done

However, there's a better way than calling awk 3 separate times:

while IFS=, read -ra fields; do
    printf "%s\n" "${fields[@]}"
done < "$file" 

• the while loop, with the file's contents redirected into it, loop over the lines of the file
• IFS=, instructs the read command to do word splitting on commas
• read -r means to not interpret any special characters as anything but regular chars.
• read -a fields reads the words in the line into an array variable named fields