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Tatraivam sati kartaaram aatmaanam kevalam tu yah;
Pashyatyakritabuddhitwaan na sa pashyati durmatih.

Now, such being the case, he who, owing to untrained understanding, looks upon his Self, 
which is isolated, as the agent, he of perverted intelligence, sees not.

This shloka is the second part where Lord talks about what happens to those who do not understand the importance of the five causes that contribute to an action. Previous shloka talked about the five causes playing a role whether that action is performed in a proper or an improper way. In this shloka Lord says that a person who is untrained and who misunderstands things regard only soul as an entity which is responsible for all the actions that are performed. Even for a wrong action also the person attributes it to the soul. This is happening mainly because of the perverted intelligence of a person who cannot see things the way it should be seen. 

Extending Interpretation to Mankind’s Life!

Who is the person with perverted intelligence here? The understanding of that is very important to understand the context of this shloka. A perverted intelligence is something that looks for the benefit, this benefit can be for the self or for a person closer to him like family or for wealth. When you gain knowledge about spirituality, it should make a person surrender to God. But many times a person channelizes it to himself and emerges as a knowledgeable and wise, increasing his own popularity. This is mainly because of the perverted intelligence. Perversion here is from the five causes to one cause that is his soul. 

Soul has urges and senses fulfil them. sometimes, the urges of the soul are directed towards an individual than towards God. This happens mainly when soul becomes the victim of senses and not the paramatma inside it. You might argue that how can soul, which has the paramatma in it be corrupted. Understand that soul is a constant seeker of knowledge and when the knowledge that soul received is limited it will be in darkness. It needs knowledge which should act as enlightenment for it to see the paramatma inside it. Till that is achieved it is incomplete and that might lead to the perversion and that is what is called as perverted intelligence.