Others may have command-line solutions. Here's one in python, untested, that I think should do what you need.

Fasta files:

one.fasta

>miRNA1
AGTCGTCA
>miRNA2
AGTTCGTT
>miRNA3
AGTCGTGA

two.fasta

>miRNA1
TTGACT
>miRNA2
AGTCGTCA

three.fasta

>miRNA3
TTACATT
>miRNA5
TTGACT
>miRNA3
AGTCGTGA

First, make a file with all the unique sequences from each of your fasta files:

cat file1.fasta file2.fasta file3.fasta | grep -v '>' | sort | uniq > all.txt

Save this code as comp_seqs.py , and run as python comp_seqs.py > output.xls in the location that has the three fasta files, and the new file with all the sequences:

#!/usr/bin/env python
import regex
from collections import defaultdict
from itertools import izip

def open_fasta(file):
        """ Open fasta file, and store in dictionary, as {'sequence:header'} """
        s = {}
        with open(file, 'r') as fasta:
                for line in fasta:
                        if line.startswith('>'):
                                h = line.strip().split('>')[1]
                                n = next(fasta).strip()
                                s[n] = h
        return s

def hamming_distance(s1, s2):
    """ Count number of mismatched characters in equal length strings. """
    if len(s1) != len(s2): raise ValueError('string lengths do not match')
    return sum(a != b for a, b in izip(s1, s2))


def find_seqs(fh, p):
        """ Find sequences from 'all sequence list' that either match as identical sequence, or mismatch of 1, store as defaultdict [{sequence:[id1, id2, id3...]}] """
        seqs = open_fasta(fh)
        for i in seqs:
                if i in x:
                        match[i][p] = seqs[i]
                else:
                        for j in x:
                                if len(i) == len(j):
                                        if hamming_distance(i, j) <= 1:
                                                match[i][p] = seqs[i] + '+1'

# Open concated fasta file, containing unique sequences
with open('all.txt', 'r') as a:
        x = [line.strip() for line in a]

# empty defaultdict for reulsts
match = defaultdict(list)

for i in x:
        for n in range(3):
                match[i].append('')


# Open each fasta, and search for sequences in 'all sequence list'
find_seqs('one.fasta', 0)
find_seqs('two.fasta', 1)
find_seqs('three.fasta', 2)

# Print results in tab delimited format
print 'Sequence\tFile1_ID\tFile2_ID\tFile3_ID'
for m in match:
        print m, '\t', '\t'.join(match[m])

Output from example above:

Sequence    File1_ID    File2_ID    File3_ID
AGTCGTCA    miRNA1  miRNA2  
TTGACT      miRNA1  miRNA5
AGTTCGTT    miRNA2      
AGTCGTGA    miRNA3      miRNA3
TTACATT             miRNA3