Stanford takes his ballpoint pen from his pocket to write on the lab plans, but in a close-up he uses a red marker, and in the next scene his pen in still in his pocket.
When Bill Cipher is choosing his next pawn, Soos is briefly shown as a potential target even though he's depicted inside the cabin. That would make him an invalid target. At the moment, he is a valid target, since he is outside the cabin. However, the pictures that Bill scrolls through are clearly just head shots, not in any way depictions of where those people currently are.