Over the past year, the LDS.org website on church doctrines has had controversial (among believing LDS people) material added to it. This includes,
Multiple First Vision Accounts:
This details the changes in the first vision stories told by Joseph Smith. You can see the story evolve, to become grander. Why didn't Joseph mention all the details at first? He had plenty of followers at that point. Soon, I'll go over the contradictions with this and the details given by other prophets about the first vision.
Details of the Translation of the Book of Mormon:
This indicates that Joseph Smith used a "seer stone" and not the Urim and Thummim for parts of the translation. This would be the same seer stone that he used unsuccessfully for "money-digging". So, we can only assume that the Book of Mormon is as accurate as his use of a seer stone.
The Changes to Priesthood Doctrines:
As most of us know, the ability to be sealed in the temple for people of African descent was only begun in 1978 by the LDS church. In this, they seem to ignore that the church believed that people who weren't white were cursed. In fact, the Book of Mormon had a recent rewrite to remove all the references of "white" and skin color changes in it. The Book of Abraham bans blacks from having the Priesthood, according to standard LDS interpretation of that scripture. For being "the most correct book[s] on earth", the scriptures sure seem to be wrong.
Polygamy in Early Utah:
This article seems to try to justify polygamy in early Utah. It points out a scripture from Jacob in the Book of Mormon, without citing the prior scripture about how polygamy "was abominable" for the mormon god. It puts the start/end dates to polygamous marriages later than they started and earlier than they began. For example, Joseph's relationship with 16-year old Fanny Alger began around 1833. The article downplays Joseph's role in polygamy, by stating "in some cases blah blah blah occurred", without mentioning that those cases happened with the early church leaders. In addition, the article gives no solution as to why women were taken from men who were already married. (Poor Henry Jacobs.. he had his wife taken twice! By both Joseph and Brigham!)