how to populate external SD for Android
It sounds like your filesystem is being corrupted by whatever else you're using to write to it with the external card reader. Probably you need to be sure to unmount the device correctly before removing the card from the reader. For example, in Windows you need to select "Safely remove hardware".

When you write files to the SD card, from any kind of computer, the writes happen in the background: like when you're noting down what someone tells you, you're always a few seconds behind them. Removing the card before the write is finished is like snatching the paper away as soon as you're finished talking, before you write down the last few words. The "safely remove" operation, whatever it's called on your OS, ensures all writes are finished.