In theory the FTP server may lock the uploaded file from being accessed by other processes or other FTP connections.
In practice, it's not happening on *nix servers. I've tested this on CentOS with PureFTPD and ProFTPD (the most widely used *nix FTP servers). With both servers, nothing prevents you from downloading an incomplete file.
On the other hand, Windows IIS FTP server does lock the uploaded file. Tested on IIS 6.2 (Windows 8.1).
Upload data files to temporary (“upload”) folder and move them atomically to target folder once the upload finishes.
Upload data files to distinct temporary name, e.g. with .filepart extension, and rename them atomically once the upload finishes. Have the automated system ignore the .filepart files.