Ok-well-- looks like a more complicated issue than just file upload incompatibilities and you’d need to give more information.
What file type are they, DICOM?
Can you upload a single image file to some arbitrary directory in a patient’s Document tree? In order to have them grouped as desired you may need to create a new directory in the patient’s Documents tree named the same as the one they came from. Then upload the individual files to each new directory.
Did you try simply zipping the individual files into an archive and uploading that zip file? I.e., don’t try to upload the directory itself.
This thread in particular, talks about php dependencies and MIME whitelisting.
A search of this forum
https://community.open-emr.org/search?q=file%20upload
brings several results, any of them ring a bell?
Best- Harley