We could add a flag --skip-open-files say.
Let's say you backedup BIGFILE successfully once. On the second time you backup BIGFILE is open so rclone misses it out from the directory listing because you were using --skip-open-files. What will happen then is that rclone sync will delete BIGFILE on the remote which probably isn't what you wanted.
That's why rclone works the way it does (this behaviour was copied from rsync).
On linux you can read an open file. You can sometimes read an open file on Windows too depending on how the application opened it.
The ideal solution on windows is probably to use volume shadow services which @asdffdsa wrote a nice HOWTO on