I know that this has come up before, can't remember if there was a solution. It requires that the PBX send Reason: SIP ;cause=200 ;text="Call completed elsewhere" and for the phone to respond appropriately by not displaying a missed call.
I do remember some complaints abut that before (perhaps some feature suggestions), I don't remember if a change was implemented in one of the newer versions. I find it is getting harder to do a search, on the 3CX site, and actually find, a topic that you know is somewhere in the Forums. I do see the same thing happening on my Linksys SPA942s.