Hey there I just made a small three line addon to do this but figured you or other people might want to fix this issue. It really isn't a bug just something that is kind of annoying and I think this is an appropriate place to put this. At any rate what I am referring to is when you hit enter and the chat box is open. First off it covers the top most part of the chat frame which is kind of annoying. Second off when there is a link in chat for an item/achievement/skill link/pattern link (I think you get the idea) when you click on the link the chateditbox hides behind the chat frame making it plenty annoying if you have typed stuff out in the box already and aren't quite finished with what you were typing. So what I did was just make a three line addon containing these lines which fixes both those issues.
ChatFrameEditBox:SetPoint("BOTTOMLEFT", "ChatFrame1", "TOPLEFT", 0, 3);
ChatFrameEditBox:SetPoint("BOTTOMRIGHT", "ChatFrame1", "TOPRIGHT", 0, 3);
ChatFrameEditBox:SetFrameStrata("TOOLTIP");
the frame strata can be changed to something other than tooltip I just wanted to pick the highest strata there was to see if that fixed the issue I haven't tried to set the strata any lower though. Hopefully this helps someone out who had/has the same issue and finds them annoying.