Why do Embryonic stem cells have increased expression of alkaline
phosphatase? It is a marker often used to identify stem cells, but I
do not know why stem cells have this increased expression of alkaline
phosphatase. Please include any link or reference if you find the
answer.

Maybe modification of ion forces can lead to activation of some cascade ;).

You asked a very broad question. "Why".

I don't know whether aklaline phosphatase shows increased expression
in embryonic stem cells but I think that it is used as a marker
because it is a specific type of alkaline phosphatase which helps to
make the distinction. I have given 3 links below:

1) This is a Swiss-Prot database entry of the enzyme which gives more
detailed information for this enzyme than other databases:
UniProtKB/Swiss-Prot entry P10696
http://www.expasy.org/uniprot/P10696

2)This article gives good information about human embryonic stem cells
and the part about alkaline phosphatase as a marker has been quoted
below:
Human embryonic stem cells
Martin F. Pera, Benjamin Reubinoff and Alan Trounson.
http://jcs.biologists.org/cgi/reprint/113/1/5.pdf

"In humans, there are four different isozymes of alkaline phosphatase.
EC (embryonal carcinoma) cells express the tissue non-specific form
and a form of the enzyme that can be detected by antibodies that react
with the germ cell or
placental form (available immunological reagents do not distinguish
between these closely related isoforms). It is not clear which form of
alkaline phosphatase the human ES(embryonic stem) cells express."


3)This articles talks about the presence of a distinctive type of
alkaline phosphatase in human placenta:
Expression of Alkaline Phosphatase Loci in Mammalian Tissues 
David J. Goldstein, Caprice E. Rogers, and Harry Harris 
http://www.pnas.org/cgi/content/abstract/77/5/2857