I first noticed the issue last year and, as a typical bloke of a certain age, I ignored it hoping it would go away. Well it hasn’t! My leeks have vertical brown stains and there are small brown pupae distributed throughout the plants. There are also a lot more external leaves which need to be removed.
This is caused by the Allium leaf miner which is fast becoming a serious pest affecting all of the onion family. It’s primarily a problem with leeks, which are its preferred host, but it will go for onions, garlic, chives and shallots. It can be devastating to the crop.
According to the RHS there are no chemical controls currently approved for its control available to home growers. The only practical control is to cover the crop, especially in the danger periods of March to June and September to November, with insect protective mesh or fleece.
If the infestation is detected in the crop, affected plants should immediately be uprooted and burned. You should not compost infested plants the pupae will still be able to hatch spreading the infection.
Further information about this pest can be found here.