I had read that some of the biggest problems in Africa and the Middle East today stem from the fact that the current nations there reflect the way that the Europeans divided their colonies instead of the preexisting conditions of those regions before they were colonized. What I want to know is, if that is the case, how come they kept those colonial boundaries instead of establishing new ones?
You should read this post about the Middle east portion of your question. http://www.reddit.com/r/AskHistorians/comments/2czcwo/objections_to_the_sykespicot_agreement/cjku3ze
As for Africa, there were a few problems. One, not all colonizers pulled out of Africa at the same time so some countries were still colonies while others were independent. Two, while many of the European nations used a system of indirect rule when governing their colonies, this again wasn't the same in each country, so even former colonies of the same country might have difficulty communicating. Three, when the Europeans left, many of them left behind governments that were ineffective or completely corrupt, and the ones that somewhat worked were often so overwhelmed by independence that they couldn't bother with worrying about the borders. Take the Democratic Republic of the Congo and Rwanda as examples. The DRC became independent from Belgium in 1960 and almost immediately had to deal with infighting in the government as well as the secession of Katanga Province, the threat of civil war, and increasing pressure from many Western countries as well as the Soviet Union. Neighboring Rwanda was technically independent(ish) from 1945 onward, when it became a Belgian "trust territory" after being a Belgian, and previously German, colony. In 1959, the Rwandan Social Revolution led to a mass exodus of Tutsi people to Uganda due to a takeover of the government by Hutus and resulting acts and threats of violence against Tutsis. By 1961, Rwanda had become an independent republic and was continuing to deal with the threat of civil war, the separation of Rwanda and Burundi, and persistent violence between ethnic groups. Really, most former colonies just didn't have the time or peace required to sit down with neighboring countries and redraw boundaries--the damage had been done.