You can change this behaviour in the Configuration -> POP3 Download -> (Select account) -> Edit -> Drop duplicate messages option.
If you use a single POP3 mailbox from your ISP for all your users, then sort them into seperate mailboxes at Kerio MailServer, there are some limitations to be aware of.
If you select "Drop duplicate messages" in the POP3 Account settings, then mails to multiple users on the server will only be delivered to one recipient. Alternatively, if you do not select "Drop duplicate messages" then all recipients will receive a copy for each recipient specified.
If you switch to receiving mail directly with SMTP, you will not see this issue at all. Also, you could use ETRN to collect your mail, but this must be supported by your ISP.