Most USB sticks are of very poor quality useful only for passing documents between devices or for use as a bootable installer. Even the better quality USB sticks should not be used as a work area as most tend to be very slow as well. USB sticks should never be used to hold the only copy of a file.
You can try running Disk Utility First Aid on the physical drive as well as the volume. If you used the APFS file system, then run First Aid on the hidden Container as well. See the following Apple article for details since Disk Utility hides the physical drives & containers from view by default:
How to repair a Mac storage device with Disk Utility - Apple Support
Also, even if the First Aid summary says everything is "Ok", click "Show Details" and scroll through the report to see if any errors or warnings are shown. If there are any, then run First Aid again until they are gone. If after several scans, the errors/warnings remain, then they cannot be fixed.
Have you tried copying those items to your internal SSD to see if you still have the same issue?