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]

A drawback, especially one that was not at first apparent: “Sharon's lack of experience turned out to be the fly in the ointment when she applied for the job.”