

Actually, just after the FIRST world war, many Muslims were killed by Serbs.
Under Serbian-led regime between the two world wars, many Croats were
also killed (especially during the dictatorship introduced on Jan. 6, 1929).
Some Croats formed a resistance movement "Ustashas" (Insurgents) and
were forced into exile, to fascist Italy, which sheltered them.  In exile,
they practiced a terrorist approach to liberating Croatia; while Croats in
Croatia followed the approach of peaceful negotiations under the leadership
of Vladko Macek.  After the Axis powers took control in the SECOND world
war, Vladko Macek refused to collaborate, so Ustashas were brought in 
to run the newly formed puppet state.  This state included both Croatia and
Bosnia-Herzegovina, and its ideology saw Muslims as the best Croats
("flowers of Croatian people").  Some Muslims in Bosnia-Herzegovina
therefore joined Ustashas.  However, even more others did not; they
joined Tito's Partisans.    The Ustashas membership peaked at 
less than 1% of Croat and Muslim population of that area at that time.

After WWII, Muslims were still considered a religious minority descended
from Croats or Serbs who converted to Islam centuries ago.  But, in 1968,
it was decided that forcing Muslims to declare their nationality as
either Serbs or Croats is not a good policy.  Dobrica Cosic, the current
president of the rump Yugoslavia, was strongly opposed, and sought to
prevent the category "Muslim" (in an ethnic sense) from appearing on the
next census.  He was criticized and expelled from the party.  So, since
that time, Bosnian Muslims are considered a separate nationality, although
some still deny this and insist that they choose either Serb or Croat
nationality.