Answer: Without seeing the fruit, I'd venture that the problem is cultural and due to wide fluctuations in soil moisture during the development of the fruit. There's an off-chance that the problem is caused by the Citrus Peel Miner (Marmara salictella Clemens). Eggs are deposited singly on the stem or more preferably citrus peel and hatch in about 5 days. The eggs are very small, oval in shape and convex on top. They are whitish in color and the top has some indistinct sculpturing. The number of eggs produced per female moth is not certain, but some have laid 7 to 12 eggs over a 4-day period.
The larvae exit the egg from the bottom and immediately burrow into epidermal layer of the peel. Thus they are never exposed. The larvae will extensively mine the peel of the fruit while passing through 6 instars. The 6th instar cuts out of the mine and lowers itself via a silken thread, to the ground or niche on the tree to pupate. The larvae complete their development cycle in 20-28 days.
You might want to further inspect the affected lemons to see if you can find tunneling between the rind and the pulp of the peel.
Hope this helps solve the mystery!
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