Has the Roman Catholic Church ever officially condemned the Croatian Ustashi? I understand the Ustashi (or Ustaše) to have been a fascist organization that dominated Croatia during World War II.  This Wikipedia article reputes that Ustashi persecution of non-Croatians was so severe that the Nazi occupiers actually had to intervene to protect some persons.  

One Eastern Orthodox Synaxarion commemorates several Serbian Eastern Orthodox clergy whom it claims were tortured and killed by the Ustasi:


Bishop Platon of Banjaluka was shod with horse shoes and forced to walk several miles before having a fire lit on his chest by Ustashi members
Bishop Sava of Krushedol was tortured and killed in an Ustashi concentration camp
Abbot Raphael Momchilovich was tortured and killed in an Ustashi concentration camp
Priest Branko Dobrosavljevich was killed with a hammer blow to the head, after witnessing the killing of his son at an Ustashi concentration camp
Priest George Bogich was strangled with his own intestines by Ustashi torturers
Priest Dane Babich was flayed and left to die by Ustashi torturers


This article from Veterans Today provides some of the gruesome details of the above and other atrocities committed by the Ustashi.  The article claims – with quotes from multiple sources – that many of the atrocities instigated by the Ustashi were prompted by Roman Catholic clergy members:


  Fra Marko Zovko consistently instigates the peasants to murder and rob
  the property of Serbs, patronizing them:“If only one Serb stays alive
  after the war, you will be paying the high price. That is why all
  Serbs must be exterminated“. Ante Pavelic, the Croatian fuhrer,
  decorated fra Zovko with the Order of Merit of the second degree.
  
  Catholic atrocities began with the destruction of Orthodox Churches as
  well as executions of Orthodox priests. Priest Samardzich  was killed
  in Kulen Vakuf. Ustashe kiled his wife and children before his own
  eyes, before killing him. Martyr’s death was destined for priest
  Milosh Vuich with many other Serbs from Slunj area. His wife was
  ripped apart, her unborn baby was taken out of her womb, another
  two-year old child was muredred as well.


Atrocities by rogue members of clergy from both east and west is nothing new, of course, but the aforementioned Wikipedia claims that the Ustashi was actually supported by the Vatican during and after World War II. In 1998, Pope John Paul II beatified Cardinal Alojzije Stepinac, Archbishop of Zagreb, who, according to some sources complied in the forcible conversion of Orthodox Serbs to Roman Catholicism.

There seems to be a lot of material on the web and in print that connects the Roman Catholic Church with the Ustashi, but frankly some of this seems quite incredible.  

Has there ever been any official communication from the Vatican condemning or denying the atrocities carried out by the Ustashi that some have connected to Roman Catholic clergy?
All official statements of the Vatican from 1909 to the present are recorded in the Acta Apostolicae Sedis (AAS). Performing the following Google search on the PDFs of the AAS volumes:

Ustaše OR Ustashe OR Ustashas OR Ustashi OR Ustaša inurl:http://www.vatican.va/archive/aas/documents/

reveals that the AAS volumes have not mentioned the Ustaše.

See also my previous answer.