Alright, let's keep the traditions of Newcomer's Necromancy and share some thoughts.
Assuming that the aliens are not martian natives, it can be possible (in my headcanon, at least) that the aliens from UFO Defence/Enemy Unknown and TFTD can be two different expeditionary forces. Bearing this in mind it's possible to see TFTD aliens as some sort of ancient lost expedition and UD aliens as more "modern" taskforce. Anyway there is absolutely no any explanation or any single hint about if martian HQ knows exactly where their predecessors went missing (sort of "they travelled to this galaxy/system/planet and then we've lost contact with them") or even that somebody of their kind visited Solar System before. The only thing we can be sure about this is the fact that Sectoids and Aquatoids are genetic relatives.
So well, if T'leth inhabitants/crew are the lost expedition and martian HQ ever heard about them... Then Cydonia could be searching for their predecessors but the conquest is their primary objective, so search&rescue mission can be "underfunded" and it's progress can be poor (because most crafts and personnel are busy fighting our glorious X-Com). The Overmi... sorry, The Big Brain couldn't waste it's resources for broadcasting the "T'leth-1, it's the Martian HQ, report immediately" message, so perhaps it deceided to look for them after the Earth will be conquered and nobody will shoot down their precious supply ships. And then SUDDENLY X-Com knocked Cydonia's door. Realizing that everything is lost, the Big Brain finally made its pre-mortem "T'leth-1, it's the Martain HQ, we got our assess kicked, take care of yourself" broadcast (there's nothing to loose anymore, so why not).
It's a real shame that TFTD's rushed development feels not only in the numerous bugs here and there but in the plot holes like this as well. Actually we can be theorizing forever until somebody will come here and deliver a word of God. Fan theories are good but hell, it's a creator who should explain everything, not the fans. As the friend of mine told once, "damn, they made a game about aliens, got cash and then the publisher came and ordered one more game ASAP - and they made the same game but switched from UFO paranoia to "SeaQuest meets Chutlhu Mythos". The End."
UPD.: I just found out TFTD Draft Publishing Plan and suddenly remembered that I saw the indroduction text years ago. Hell yes, it says that T'leth
is the lost expedition ("the remains of a vast colonization ship"). I guess the aliens used MC to make me forget this
