There are "difficulties" and misunderstanding about a lot of Bible verses, and some of the most complex and interesting are in Genesis. 

Genesis 1:1- the actual point of creation.  In science, it is called "THE singularity" (a singularity is a zone that cannot be explained with our current understanding of physics).  The theory of the Big Bang works perfectly mathematically until it goes back it time towards the actual point of creation.  Thus far, science cannot explain the actual moment of creation.  The same problem arises with the scientific law "energy is neither created nor destroyed."  The math falls apart at the actual moment of creation.  So, the Biblical explanation does NOT contradict with the scientific explanation.  However, many scientists are starting to disbelieve the Big Bang theory due to the fact there are many contradictions.  Research and theories are constantly being developed and are beyond the scope of this book.

Genesis 1:1-5- were the "days" and "nights" literally 24-hour periods?  (See Genesis: Chapter 2 for more complete discussion). 

Genesis 1: 13-18- the sun wasn't created until the third day, but God separated the light and darkness on the first day.  There are two explanations often put forth: 1) God Himself was the source of light prior to the creation of the sun  -and/or-  2) God had already made the sun prior to this point and it was providing light, but it wasn't until the third day he put it in it's current position (1:17 "set them in the dome of sky"). 

Genesis 1:26- God refers to Himself in the plural when he says "let us make man in our image."  This is simply how the Hebrew language uses the word.  "Us" is simply a more majestic form of "I"....not an indication of multiple Gods, references to the angels, or any other crazy theories (aliens, for example).  Many Middle Eastern languages work this same way.  Some claim that the "us" is a way of proving the existence of the trinity, but that is a misunderstanding of the translation.  Other Old Testament verses more clearly foreshadow the trinity.