Because a human vessel with a mostly-human crew totally screwed up their battle plans on three separate occasions and even managed to kill one of them. So either the Reapers are scared of humans and want to make sure to overwhelm them so they can't pull some other trick out of their sleeve (which they wound up doing anyway) or they're really PISSED OFF at the humans and want to make sure they get hit the hardest of everyone. Either option is fits Harbinger's final threat from ME2:
Human, you've changed nothing. Your species has the attention of those infinitely your greater. That which you know as Reapers are your salvation through destruction.
It's probably a combination of both: the Reapers have noticed the tendency of humans to throw monkey wrenches into their plans, which has them both nervous and angry.
Plus they were probably aware of the Prothean archive on Mars by that point and seeing as the Prothean Conduit project allowed them to set the Reaper's plans back considerably as well as leading to the loss of the element of surprise which made their quick massacre turn into a probably lengthy war of attrition they probably want to make sure the Protheans did leave anymore final postmortem "f@#k you"s laying around.