In the LDS temple endowment ceremony, there are two issues that a faithful Mormon must deal with.

First, why is the order of creation unlike that depicted in LDS Standard Works?  In the temple, the creation of plants comes BEFORE light and darkness.*

Secondly, how could Peter have given a handshake to Adam, since Peter did not yet have a body at the time of Adam, and spirits cannot shake hands?

(Thanks to a discussion on Recovery From Mormonism for these two points.)

UPDATE TO THIS POST:

Fred Anson has pointed out that to his understanding the LDS temple ceremony has the order of creation in harmony with that of the Bible; but other LDS scripture does not:

OK, I found where the confusion comes from.  This discrepancy isn't in the Temple Endowment Creation account it's in the Book of Moses account. In that account the plants are created BEFORE light is. Here you go: http://www.facebook.com/l/41d96;www.lds-temple.org/index.php?page=creation

Of course this raises the rather telling question: Why do all of the LDS creation accounts contradict each other? Let's count them:

1) Genesis account in the KJV

2) Book of Moses in the PoGP

3) Book of Abraham  in the PoGP

4) Temple Endowment Ceremony

5) Book of Mormon
(more snippets than full creation accounts, but still contradictory)

 

http://www.facebook.com/l/41d96;eom.byu.edu/index.php/Creation,_Creation_Accounts

For more information, see The Mormon Mirage 3rd Edition:  A Former Member Looks at the Mormon Church Today(Zondervan, 2009). Also available as an audiobook and as an expanded-text E-book for Nook, Kindle and other reading devices.