Hi. Since sen2cor is not issuing specific messages, at least about those missing folders, my issue might not be the same as yours. I downloaded single tiles from Google Cloud Plataform, and you have to do some modifications for those files to work correctly with sen2cor.
The first thing is to change the name of the downloaded folder to match the requirements of sen2cor (S2A_xxxx_xxx_MSIL1C_…)
So S2A_MSIL1C_… becomes S2A_OPER_PRD_MSIL1C_…
Then, inside the base folder, sen2cor also requires that two another folders be present:
AUX_DATA and HTML. So just create those folders inside the product base folder and it should work.
Another problem I was having, but only in Windows, is that file paths become to long for Windows to handle them.
So I moved the product to c:\ and processed it from there.
I was also having permission issues, so you can look if the folder is not “Read only” and also try to run sen2cor from inside a command lines started as administrator.
Hope this helps, cheers