While the general behaviour is improved, there are a lot of different cases and without seeing it first hand it is difficult to say if this is unintended or not. For example, in what you've described this sounds like the D-Day landings. Typically the AI will attempt to land all other units prior to an HQ, and HQs (if I remember correctly) will try and land only if they are not adjacent to an enemy unit. However, this is also balanced against the idea that an available city is there for capture, or the HQ might be the last available unit to hold a city (same applies to air units) and in this case as a last resort an HQ might land or hold a city if it is the only unit available to do so.
It's one of those where yes, it might be better for an HQ to not be used this way, but on the flip side, some situations might arise where one will wonder why the AI didn't take that open city and so on. It's a bit of a damned if you do, damned if you don't. But of course, this is a bit of speculation on my part since as mentioned I haven't seen the sequence play out first hand, but generally that is the thinking behind likely this type of manoeuvre by the AI.