1
fault;weakness;flaw;defect;drawback;disadvantage
あそこの食べ物はうまいし値段も安いが、地の利が悪いのが難点だね。
That place's food is great, and their prices are good, but the fly in the ointment is their terrible location.
2
crux (of a matter);difficult point;point of contention
ただし押し込む瞬間気圧の変化のせいでしょうか、耳がツンとするのが難点です。
However, maybe from the sudden change in pressure when you push them in, having your ears pop is a problem.