I like to imagine every cartoon/game with animal/anthro characters reside in the same universe so they could cross over at any time. Here, it's like: after defeating Andros, data files recovered from his base lead to Robotnik, who they believe is one of Andros' R&D agents and whose various experiment files cause Team Star Fox to believe Sonic is a living weapon created by Robotnik commissioned by Andros, which eventually leads to this misunderstanding.