I harvested my shallots soon after the leaves died but most are soft and small in size. Did I wait too long to pull them? Could wireworms be the cause? Many of my onions have soft spots, also.
Why Are My Shallots Soft and Appear to Be Rotting
Certified GKH Gardening Expert
It could possibly wireworms. If you see tunneling that is a good sign it is them.
More likely it is root rot. Shallots need excellent drainage to do well. If it was too wet in the area where they were growing, then it would cause problems like you describe.