well sometimes "clone" just means they are both playing on the same connection (e.g. brothers). the server cannot tell those situations apart - it does not know whether it is two people on the same connection or really someone cloning (connecting several OpenTTD clients to get an advantage), which is also the reason why we don't kick or ban clones but only issue a warning.
the idea is that after the warning you can watch them - is the second company by the "clone" only created to do destruction work, so that his main company doesn't get a bad rating at towns? or is it a fully active company (maybe even with activity at the same time as the company of the other player)? also if the clone joins the same company it usually is two people playing together, as for cloning this wouldn't give any advantage.
sorry for the long text, what i am trying to say is that such situations cannot be checked only by some lines of chat log, best always is to have an admin check on that situation (but please don't call an admin for every clone warning, admins see the warnings anyway).