The Lord's actions are apparently contradictory but the Lord has a definite plan behind all actions (contradictory or otherwise). I was reading this purport by Srila Prabhupada and found it very illustrative of the actions of the Supersoul. It is very difficult to mentally map the logic behind the Supersoul's dictation and control.
Srila Prabhupada writes in this regard
"For our understanding it is sometimes said that the Lord is situated in the heart of the thief as well as in the heart of the householder, but the Supersoul in the heart of the thief dictates, "Go and steal things from that particular house," and at the same time the Lord tells the householder, "Now be careful of thieves and burglars." These instructions to different persons appear contradictory, yet we should know that the Supersoul, the Supreme Personality of Godhead, has some plan, and we should not consider such activities contradictory. The best course is to surrender unto the Supreme Personality of Godhead wholeheartedly, and, being protected by Him, remain peaceful" - SB 4.17.36
Among these apparent contradictions, Srila Prabhupada ultimately concludes with the grand plan. In one sense the grand plan of all of creation. What is that grand plan? That is the conclusion of the Bhagavad Gita and also stated above at the end - to surrender unto the Supreme Lord wholeheartedly, be protected and remain peaceful among all good and bad of this world.