"When Jesus had thus said, he was troubled in spirit, and testified, and said, Verily, verily, I say unto you, that one of you shall betray me." (John 13:21 NLT)
"With Christ as my witness, I speak with utter truthfulness. My conscience and the Holy Spirit confirm it. My heart is filled with bitter sorrow and unending grief for my people, my Jewish brothers and sisters. I would be willing to be forever cursed - cut off from Christ! - if that would save them." (Romans 9:1-3 NLT)
Here is something we have to examine carefully, but not hard enough to base any sort of doctrine on, because the just of this topic is extremely, way above our paygrade! When I first started this journey, I began with a topic that is very complex and two-sided; much like a coin has two sides, but it is still just one coin.
The very first hint of this, "trouble," is maybe listed in the time of creation, between the first and the second day. Oddly enough, that is the timing of and the just of this particular subject: God's will, and God's perfect will, and the meaning of Him being troubled. In the beginning, the issue was called, "the firmament," which was something of a mystery, although some might think they have it figured out.
As I have said before, this is that first part of the creation, that at the end of the day, God did not say, "It was good." To try and understand why this might have troubled God, was the disconnect between that place where He dwells and the place where man would dwell; that He would be separated from His creation. Don't misunderstand, He had fellowship and could have a relationship, which He did; but due to the Holiness of His nature, He and the man He created were on a whole different level.
Some people believe that Heaven is really not some far off place that is way above the stars, but that it is simply another space that somehow is all around us but is outside of our time-domain. Much like Stephen, as he was dying, he saw Jesus standing at the right-hand of the Father; that was not millions of miles away but was right above him.
The second example of God being troubled, was mentioned in the second account of the 6th day, the creation on man; as God shows how He created man, and then how He taught him to care for the earth and all the other living creatures. Then, he examined man's curiosity about being set-apart from all the other creatures; as that all of them had mates, but he had none.
And then we have Genesis 2:18: "And the LORD God said, It is not good that the man should be alone; I will make him a help meet for him." Why was this not the case before? In the first mention of creation, Genesis 1:27 says: "So God created man in his own image, in the image of God created he him; male and female created he them."
Moving forwards, we come to one of the most talked about times when God was troubled, Genesis 6:6, as it says: "And it repented the LORD that he had made man on the earth, and it grieved him at his heart." Many people assume that God regretted making man, as if He had wished that it had never happened. I reject that belief, because I believe that God knows everything, and He never makes any mistakes!
Then we have the case of Hezekiah, which was the topic of the discussion when I first began this, back in January of 2010. If you don't know the story, the LORD sends Isaiah to Hezekiah, telling him that he needs to get his house in order, because the sickness he has will be his death. But Hezekiah did not want to die, turning his face to the wall, he prayed for more time.
God gave Hezekiah 15 more years to live! Two sides to the coin, but it is only one coin; oddly enough...
"So I decided that I would not bring you grief with another painful visit. For if I cause you grief, who will make me glad? Certainly not someone I have grieved. That is why I wrote to you as I did, so that when I do come, I won't be grieved by the very ones who ought to give me the greatest joy. Surely you all know that my joy comes from your being joyful. I wrote that letter in great anguish, with a troubled heart and many tears. I didn't want to grieve you, but I wanted to let you know how much love I have for you." (2 Corinthians 2:1-4 NLT)