What are the details you used in the Destination Panel?
I suspect you may have renamed the files by date, but had the 'Organize' option set to [into one folder].
Do not re-import. It is easily possible to use the Metadata Filter to select photos by date (Year, Month, Day) and drag them to appropriate folders in the folder panel. (Right-click in the folders panel to create new folders.)
The date format options in the import dialog are also very confusing (they were for me!).
Thank you for your response.
Basically, I leave each photo when importing rename. This looks like this: YYYYMMDD_HH-MM-SS_FileName
My folder structure is e.g. 2016/01 ... 2016/12 etc. As I always do.
During the import, however, the files are curiously copied partially to the wrong folder. Some photos of a series are e.g. Copied to the correct folder, others turned into a completely different one.
Sorry can not be of more help.
Another expert in metadata may be able to check if Lr is not reading the iPhone files metadata correctly.