"A fly in the ointment" is a very old idiom, probably derived (as are so many things in western culture) from the Bible:

Dead flies cause the ointment of the apothecary to send forth a stinking savour: so doth a little folly him that is in reputation for wisdom and honour.

Ecclesiastes 10

It refers to someone or something that ruins an otherwise perfectly good state of affairs. It's generally a small thing, an annoyance, rather than something huge and catastrophic.

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