Thanks for these comments, you are so right that the harvesting bit is not covered enough, and alliums are hard to assess for ripeness… or mouldiness and disease.
The two possible diseases are white rot which is serious and terminal (bright white fungus around roots, tops having gone yellow quite rapidly – burn them rather than compost), and mildew of onion and shallot, after grey mould and yellowing of leaves, then bulbs are edible for a while but do not keep. It sounds like your shallots may have the latter, which often arrives with bulbs and sets that are offered to plant. For that reason I grow most of my onions and shallots from seed. Onions should still be growing now and full of green leaf until mid July, when their bulbs are swelling fast and harvesting becomes possible, normally end month or early August, governed by days shortening above all.
Garlic are different, more like leeks, prone to yellowing and rusty orange spots from lack of moisture in April and May, as this year. I watered my Purple Wight and it is still green and healthy, was more yellow in April. Other of my garlic now has orange rust, is yellow and needs harvesting, but with reasonable size bulbs. Once the leaves are half yellow you need to pull/dig them up as they then decay from the outside (losing skins) rather than grow.
My Winter Vegetables book has quite a bit on these and other harvests. Good luck and keep growing.