This sort of thing usually happens when you plug in flash disk to old PCs (Pentium IV or lower) or on PC's internal card reader with USB port. Apparently, some old USB controllers (those that were manufactured before 4-GB flash storage were developed) simply do not support USB drives larger than 2GB. As a result, the files get corrupted.
If you can still open those folders and files then I suggest you copy those files to another drive immediately.
Before attempting to fix it, copy the files to another drive as backup.To fix, simply run
CHKDSK on your flash drive.
If you cannot recover your data through
CHKDSK then I suggest you to use a recovery software.
I just found this excellent recovery software TestDisk.
It is called TestDisk and it is a powerful recovery software. It can fix partition tables, FAT, FAT32, NTFS boot sectors, recover deleted files, copy deleted files, and many more. I suggest you go to the website, download, install and give it a try for yourself. It is easy enough to use for experts and novices alike.
Another powerful tool you can use is GetDataBack for NTFS and Fat.
Hope it helps.