A/the fly in the ointment
Definition 1 of 1
Pro Tip 1/3Spoils Perfection
Emphasizes a defect ruining something otherwise ideal. Reflects disappointment. 
They offered me my dream job, but the location was a fly in the ointment.
Pro Tip 2/3Small Scale
Highlights that the issue is minor compared to the overall good quality. 
It's a beautiful house, but being near the airport is the fly in the ointment.
Pro Tip 3/3Metaphoric Usage
Used metaphorically, not describing real flies or ointment. 
His constant lateness is the fly in the ointment of our team's productivity.