I may be speculating but here it goes. Based on what we all have seen and know so far I think we may actually be trespassing into their space. First of all those thargoid "bases" as well as most of the pre-2.4 "encounters" are well outside of human occupied space (the bubble). As for 2.4 when ships,NPC and Commander, go to the Pleiades region to investigate "non-human" signals or when interdicted from hyperspace thargoid ships do not always "open fire" more like they pause and scan you ship to "identify" you before they turn red and if they don't it may mean they don't consider you a threat and not worth it. When they do turn red before attacking it may be a warning to leave their territory or else.So those ships may just be military patrols. Those destroyed human ships may have been military, or contracted by the military that "shoot first and asked questions later" like in the 2.4 trailer in which the thargoid's back was turned and barely acknowledged the attack wing until shot at with prototype missiles. Also those "bases" may be attempts to colonize those planets/moons like our planetary ports. So all of this may be us incurring into the frontier of their "settled" space.They may not have even been expecting to re-encounter humans for another few centuries due to humans not having access to Frame Shift Drive technology not considering us reverse engineering their technology due to it being so different.