What causes lemons to have the bad spot?
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Could be a number of things. See if these links help.
http://ipm.ucanr.edu/PMG/C107/m107bpfruitdis.html
https://www.gardeningknowhow.com/edible/fruits/lemons/common-lemon-tree-diseases.htm
https://www.hunker.com/13428503/what-causes-lemons-to-be-brown-inside
I have only seen that on downed fruit that was not picked up right away. Could have been a freeze?
http://ipm.ucanr.edu/PMG/C107/m107bpfruitdis.html
Just like people - we all get spots eventually......
Never how how this stuff is treated before we buy it. It may be thrown and dropped. If we knew... we probably wouldn't use grocery store again!
It could be sunscald. Plants, like people, can get sun burn. If the lemon was protected from the sun and then for some reason the protection was removed (say another fruit had been covering it) it can burn. That's my first choice. Another could be freezer burn. Sometimes fruit can be exposed to freezing temperatures during shipping or storage. Not just on the tree.
it looks like too much water.
Age or moisture