You certainly do not have 100 % fertilized eggs when using AI. The spermatozoa have to travel all the way up the oviduct to get in to contact with a yolk with has been released from the ovary. Then fertilisation has to take place. This whole sequence is a biological process so it will never work at 100 % efficiency.

Inadequate practices during AI will contribute to failure.

One other factor also complicates the whole picture: very early embryonic death is (almost) not distinguishable from non fertilized.

There is a pretty incredible sperm selection process that occurs in the female reproductive tract. Following this, sperm survival can be affected by breed and feeding level (worse in over-fed birds!). It can be enhanced through provision of quality antioxidant feed additives. Some birds also just don't do well. We would always have a few of our AI broiler breeders that were more likely to produce infertile eggs. We always did our AI at about 3PM to avoid having an egg in the shell gland. A mass of fecal material in the cloaca could also be a problem. J.P. Brillard, M. R. Bakst, and R. K. Bramwell are good researchers to start with to learn more about some of these processes.    

this is the biology you cannot assume that 1+1=2

there are many factors that contribute with the fertilization process

There are many factors that may be responsible for this: nutrition of the rooster, sperm selection and capacitation failure in the SSTs of the hens, breed effect, joining rate, etc. Even in AI, there can not be 100%fertility.

Thank you all