The previous answer has some significant errors. Asexual reproduction is not mitosis. Mitosis only occurs in eukaryotes. Bacteria asexually reproduce by binary fission or budding. Also, while bacteria don't reproduce sexually by definition, they do regularly exchange genetic material.
Anyway, to answer your question, the difficulty with bacteria is that it makes it difficult to use the old species concept of: "Two organisms that are able to reproduce naturally to produce fertile offspring," (taken from wikipedia) since that definition requires sexual reproduction. Note there's also some other reasons why it's hard to define a bacterial species.
Why does asexual reproduction in bacteria make it hard to define their species?
Asexual reproduction, also known as mitosis, always makes identical copies of the same cell, in this case, bacteria. Every detail is the same in these bacteria, so nothing changes and this process goes on and on and on. Sexual reproduction (meiosis) involves the crossing over of alleles in homologous chromosomes (chromosomes for the same trait), creating genetic variation. Genetic variation is a random process that makes it impossible for organisms who reproduce sexually to be exactly the same. But most bacteria can't reproduce sexually, so their copies will always be the same as the one before. This makes less distinction between different kinds of bacteria. The changes between them occurred so slowly.
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