1
general::
A drawback or detrimental factor. For example, The new library is wonderful but there's a fly in the ointment: their catalog isn't complete yet. This term probably alludes to a biblical proverb (Ecclesiastes 10:1): "Dead flies cause the ointment of the apothecary to send forth a stinking savour." [c. 1600]
American Heritage Idioms
2
general::
Phrase(s): a fly in the ointment
Fig. a small, unpleasant matter that spoils something; a drawback. • We enjoyed the play, but the fly in the ointment was not being able to find my hat afterward. • It sounds like a good idea, but there must be a fly in the ointment somewhere.
McGrawhill's American Idioms And Phrasal Verbs