Seeming contradictions in the Bhagavad Gita

1) Chapter 9: Verses 4 and 5 

In verse 5 of the Bhagavad Gita, Bhagavan contradicts a statement he made in just the previous verse (shloka #5) . And he does not seem to slip this unnoticed as he had done so on previous occasions.  He seems to blatantly contradict his statement immediately after making it as though challenging the readers to see if they were paying attention.

मया ततमिदं सर्वं जगदव्यक्तमूर्तिना |
मत्स्थानि सर्वभूतानि न चाहं तेष्ववस्थित: || 9.4||

mayā tatam idaṁ sarvaṁ jagad avyakta-mūrtinā
mat-sthāni sarva-bhūtāni na chāhaṁ teṣhvavasthitaḥ

All this universe is pervaded by me, whose form is unmanifest. All beings exist in me but I am not (supported) in them. 

न च मत्स्थानि भूतानि पश्य मे योगमैश्वरम् |
भूतभृन्न च भूतस्थो ममात्मा भूतभावन: || 9.5||

na cha mat-sthāni bhūtāni paśhya me yogam aiśhwaram
bhūta-bhṛin na cha bhūta-stho mamātmā bhūta-bhāvanaḥ

And beings do not dwell in me; See my divine union (with the Universe), creating and sustaining beings, I do not exist in them.

1.1) Mithya

By making a statement and immediately negating it, Bhagavan is conveying an important message about the transitory nature of the material aspects in the Universe. This is called Mithya. Any material object in the Universe is seemingly existent but upon closer examination, is factually non-existent. Therefore Mithya is that which has a lower order of reality. This is clarified by the following two often used examples in Vedanta.

1.2) Dreams as Mithya

Dreams exist during dream state and can be terrifying, but are gone in the waking state. Therefore it is seemingly real but only exists in the imagination. Nevertheless a terrifying dream can cause perspiration and increased heart rate etc. just like when we are faced with a real danger. 

 1.3) Ornaments as Mithya

Another example that is commonly used in Vedanta is that of Gold and Gold ornaments. Take the example of a gold chain. Gold exists in a gold chain but a gold chain is not permanent in that it can be melted and made into a bracelet or a ring. Therefore the chain has no real existence and is just a name form. Gold, however, has (more) real existence. 

2) Chapter 12: Shloka 12 contradicting the order of sadhanas given in shlokas 4 through 11.

 In chapter 12, Bhagavan describes the 5 rungs of sadhana (practice) for the various levels of the seekers. Bhagavan starts off by describing jnana yoga or Nirguna Ishwara swarupa bhakti (#1) as the highest level of sadhana and is suitable only for those the prepared mind.  Then he describes Saguna Vishwa-rupa Ishwara upasana  (#2) or meditation on God as the manifestation in the entire cosmos. He, then says, that if Saguna Vishwa rupa Ishwara upasana is difficult, resort to Saguna Eka-rupa Ishwara Upasana (#3) for which he gives the term Abhyasa yoga, or simply mechanical meditation without knowledge. At the fourth level from the top, he describes Karma Ishwararpanam (#4) or offering one's actions to Ishwara as worship. At the bottom of the ladder, if one finds the above forms of worship as too difficult to perform, he describes, karma phala tyagam (#5) or renunciation of the fruits of actions as a valid form of worship even though it has little to do with Ishwara or Brahman. 

Then, in an unexpected twist of events, Bhagavan gives a different gradation of sadhanas for those who find the above comprehensive list too difficult. This time, instead of grading from the highest to the lowest level of sadhana, he grades it from the lowest to the highest. He skips Nirguna Ishwara Swarupa Jnanam because it is meant for the highly accomplished and prepared mind. He, then, puts Karma phala tyagam or the renunciation of the fruits of actions, which was the lowest rung on the comprehensive ladder of sadhanas, as the highest. Swami Paramarthananda says that this is one of the most confusing shlokas in the Bhagavad Gita, so much so, that it can feel like it would have been better if it were not there. 

However Krishna does this to encourage people, most of whom are ready for the lowest step only, to at least perform Karma phala tyagam, instead of not engaging in any spiritual practice. In sanskrit, this is termed Atishyokti (अतिशयोक्ति) which can be translated to "exaggeration" or "hyperbole".  And for this reason, the whole shloka is called arta-vāda slōkāḥ which means exaggerating the value of a sādhāna to encourage the people to practice that. Bhagavan seems to say "small is beautiful" to encourage people to take up simple practices.