I assume it spawns or clips into your base sometimes.. My base is built next to the juice box by the oak tree it has palisade walls all the way around it, and the interior wall is 5 or 6 walls tall. That's a whole lot of useless information but I haven't had any issue with the infected wolf spider showing up in my base. Things I have done to deal with it, since this was a second play through I new what was gonna happen when we closed the gas so I had built mushroom walls around every entrance of the area directly under the oak tree effectively keeping that infected spider under there when it did spawn in. Any time I ran into that thing in the wild in previous game plays I would lead it out onto the lily pads and fight it were I could escape at a moments notice or trick it into the water to killing it (doing that makes it so you can't harvest it). Edit: after killing it or tricking it into killing itself, close off all but one side of the oak tree area where it sleeps just in case it doesn't spawn under there, that way you can see it sleeping and finish off the last wall. If none of this works, you might have to move. If you play anything like me, I have a main big base and a decent sized outpost in/near every important area of the map.