Whenever I hear "at it" or use it myself, it means I am describing an action or task, but giving it a bit of a sense that the person is either senselessly doing something, or even overworking. It sort of means to persevere at something.
Example, if I'm swamped with housework, and I really ought to take a break, my husband might say to me: "I see you're at it again?" It almost sounds like I'm doing more than I should and should be done in moderation.
"At it" can have some negative meaning too. If the couple across the street are having a loud argument, and this is a common thing that we have to listen to as neighbours, I might tell my husband: "That couple across the street is at it again." We understand it means that they're fighting, because it's really all that we know that they do.
"At it" can also be belittling. Someone might be doing a task that they think is important, but saying "at it" reduces its importance if asked about it. For example, if someone is knitting a scarf, and they just make mistakes, and unravel, and redo it over and over, they might be asked: "You've been at it all night. Just quit."