Generally, considered to be an advanced firewall, CSF blocks external IPs (Inbound Connections) to avoid Brute force attack or attack similar to that (Multiple login failures, hacking attempts, etc.) on a server. The firewall might block the connection while uploading files using Filezilla. It might be possible that Filezilla is trying to open multiple simultaneous connections to speed up the transfer. The firewall may interpret it as brute force or port scan activity and block the IP address from where the connection is originating.
Securing web server is the most vital and important part if it is facing flood attacks. If the server is available over the Internet without any protection, then a regular flood of random and targeted attacks is going to happen. That is the reason installation of a firewall and a brute force attack detection tool should be considered at very initial stage. In the present situation we recommended CSF and LFD to secure web server. Both tools have keep up with the pace and are very much updated. And the best of all this solution is freely available.