We have a vendor-specific device for USB connections.
We used LibUsbDotNet Bulk Transfer communication. In the first case, I did 64 byte data transfer. In the second case I made 1024 byte data transfer. In case of 64 byte transfer, there is usually no problem (Problems are rare). In case of 1024 byte transfer, there is a problem (almost always in USB 2.0 port, also rare in USB 3.0 port).
What causes to this problem?
When data is in multiple of 512 bytes, add an extra dummy byte to the data. So if you are transferring 1025 bytes your problem will be solved.