Try this one.

#!/bin/bash

# Run it in the folder containing dir A and dir B.

A=A #first dir, replace with the propper name
B=B #second dir, replace with the propper name
in_file=f #replace with propper name
out_file=data.dat

B_subs=( $(ls B | sort -n) )

i=0
cd "$A"
for d in $( ls | sort -n) ; do
    a="$d"/"$in_file"
    b=../"$B"/"${B_subs[$i]}"/"$in_file"
    ((i++))
    mkdir ../"$i"
    join "$a" "$b" | awk '{print $1, $3-$2}' > ../"$i"/"$out_file"
done

Try this one.

#!/bin/bash

# Run it in the folder containing dir A and dir B.

A=A #first dir, replace with the propper name
B=B #second dir, replace with the propper name
in_file=f #replace with propper name
out_file=data.dat

B_subs=( $(ls B | sort -n) )

i=0
cd "$A"
for d in $( ls | sort -n) ; do
    a="$d"/"$in_file"
    b=../"$B"/"${B_subs[$i]}"/"$in_file"
    ((i++))
    mkdir ../"$i"
    # the one below is not correct, but gives your results
    # join "$a" "$b" | awk '{print $1, $3-$2}' > ../"$i"/"$out_file"
    # the one below is correct
    join "$a" "$b" | awk '{print $1, $2-$3}' > ../"$i"/"$out_file"
done