I recently harvested leeks and was horrified to find them riddled with little orange bugs. They had bored into the stem & the whole stem was distorted. Looked it up on the web & discovered they are Allium Leaf Miners.
Trouble is they overwinter in the soil & then affect all members of the allium family – so there goes my shallots, garlic & onions next year. No chemical controls either ….. The only suggestion is to do a strict crop rotation & to cover the plants at two critical periods in the lifecycle of the pest viz. March-April & October – November.