The Spinning Tractricoid is actually Mal's totem. The reason why it kept spinning is because she lost track of what is real and what is a dream.
Cobb claims that it is his totem. However, he is sure not to make anyone touch it. It is likely that Mal has gotten rid of her totem because she enjoyed the dream much more than reality. It is likely that Cob took the totem but never replaced his own.
When Cobb is dreaming, he's often seen wearing a ring. This is thought to be his totem, not the Spinning Tractricoid. He does not wear the ring in reality.
Cobb convinced Mal to go to limbo with him. In that dream, they have lived a lifetime which drove her insane. She became convinced that reality is actually Limbo.
Cobb likely lost control over his subconscious as shown by Mal throughout the dreams. It might be the reason why his ring is never shown in reality.
Cobb actually wakes up at the end of the Inception and returns to his children. However, the spinning totem is a symbol of his damaged subconscious and Mal's madness.
According to several fan theories, Cobb hid Mal's totem to convince her into going to limbo with him. Thus, he drove he insane when they returned from a lifetime of living alone in a dream. According to the theories, his guilt is what leads Mal to attack him in dreams.