Does Ubuntu damage USB drives?

No worries Ubuntu did not damage your USB drive. But we do not use poorly documented bit flags of a FAT32, FAT16, or NTFS filesystem. On Windows these flags indicate a possibly corrupted filesystem when we had not properly unmounted the drive or an I/O error had occured.

Those bits are located in a reserved entry of a FAT partition table. According to an internal Microsoft paper of 2004 the purpose of these bits are:

• ClnShutBitMask:
  If bit is 1, the volume is “clean”. The volume can be mounted for access. If bit is 0, the volume is “dirty” indicating that a FAT file system driver was unable to dismount the volume properly (during a prior mount operation). The volume contents should be scanned for any damage to file system metadata.
• HrdErrBitMask:
  If this bit is 1, no disk read/write errors were encountered. If this bit is 0, the file system driver implementation encountered a disk I/O error on the volume the last time it was mounted, which is an indicator that some sectors may have gone bad. The volume contents should be scanned with a disk repair utility that does surface analysis on it looking for new bad sectors.

There was some discussion with the kernel file system developers some years ago on how to overcome this but I was unable to follow up the results. Apparently it did not make it into recent kernels.

As only a bit flag is involved but generally our data should be in perfect shape we can ignore the warning Windows issues on those drives we had previously used in Ubuntu.

This is mostly an issue with Windows. It thinks it is the only OS in the world and acts out if it detects something it does not understand.

Just because Windows says you must repair the drive does not make it true.

Any of my drives used with Ubuntu get this message from Windows, I just say no and they work fine with Windows.

In short there is nothing wrong with the drive, it is just there is something on there that Windows does not understand and its response is destroy it.

Don't repair the drive, it will format it without telling you and you will lose all the data on the drive.

As you suggested in a comment, this is possibly related to Ubuntu not completing the write process before you remove the flash drive. Ubuntu writes the files to RAM during the copying process, and writes these files from the buffer to the USB drive in the background after the copying dialog is closed. There's another answer that suggests this is especially a problem for machines with large amounts of memory, but it's likely that you're removing the drive before the background write is complete. When you eject a drive, this forces the buffer to be written to disk, but it is difficult to tell when the write is actually completed. There's a pop-up in newer versions (15.10 for certain, possibly 15.04) intended to remedy this -- a purple alert appears after some (generally short) time that says something along the lines of "[Drive] can now be removed" once the write is finished.

This is probably the reason your friend suggested sync. Running sync in terminal forces all buffered data to be written to disk, and should return only once the writes are completed (See this answer). See this answer for a utility that will help you determine if this is actually the problem.

I've seen lots of usb drives, especially flash (SD, etc) cards in USB adapters, with FAT filesystems (virtually every USB drive comes pre-formatted with FAT32) getting corrupted while using Ubuntu & Ubuntu-derived distros. It was almost a regular occurrence every few months of regular daily use.

If it were a hardware problem, then formatting the partitions with ext3 (or 4) shouldn't help, but ext3/4 makes the filesystems virtually bulletproof. (ext2 also was corrupted over the few months I tried it; was supposed to have less writes so a longer life for flash drives, mainly from no journal).

So, Ubuntu should not physically damage USB drives themselves, but I still don't trust it 100% with FAT filesystems.

I think filesystem corruption can be best avoided by:

• Never just unplug a USB drive until after it's been unmounted/umount/ejected. Even if the drive's not currently writing anything (if it has a light it's not flashing) and even if you've done a sync the filesystem may still
• Wait at least a few seconds after umount/eject before unplugging it. It seems that even after umount the drive's activity light may sometimes keep flashing for a little while. Other users like this guy say it could go on for up to a minute.
• Don't only rely on only sync either, like this guy who got file corruption.

Related (generally) links:

• Answer to "Should I unmount a USB drive before unplugging it?"
• Is execution of sync(8) still required before shutting down linux?
• How to remove a USB drive without worrying if its been unmounted?