There are two different versions of this photograph. In the first one, of better quality, the "milicianos" appear to have shot a hole through the pelvis of the disinterred nun and inserted a carrot or similar object (perhaps a roll of crumpled paper), mimicking an "erect penis". The militia man at top left appears to be pointing to it. If not, what is he pointing at?

In the second version, of poorer quality, the "carrot" or "penis" has disappeared, and the "bullet hole" appears to be a tear in the mummified tissue covering the pelvis.

Again

The photographs do not appear to have been retouched.
On the other hand, the "carrot" or "penis" is far too "white" to be natural (it is one of the whitest objects in the photograph), even if it is only a roll of crumpled paper.
If it is a roll of crumpled paper, it seems unlikely that the paper would be that "white". They would probably use a crumpled newspaper or pamphlet, perhaps a religious tract.
They would not have possessed reams of snow-white modern typing paper at their disposal for the task of mimicking a penis in one photograph.
Thus, I do not believe that the "penis" forms part of the original photograph.
It appears far more likely to me that the "carrot" or "penis" is a tear in the surface of a single copy of the photograph.
Yet there are no other tears: the photograph is in good condition.
My personal belief is that a single copy of the photograph was defaced by some filthy-minded "miliciano" with a pocketknife or small nail, for the purpose of giving the impression of an erect penis. Very funny.
Given some of their other stunts, this would not surprise me.
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Note:
The Spanish Civil War was fought with tremendous savagery and ferocity on both sides.
Yet I have never heard of any rapes. Rapes must have occurred, but I have never heard of any.
Tens of thousands of summary executions, but no rapes: particularly, no gang rapes of all those nuns they arrested.
In this sense, it is not true that "Africa begins at the Pyrenees".
Africans -- or Russians, or even the "idealistic" Americans -- would have raped everything in sight.
For example, tens, and possibly hundreds, of thousands of women -- both black and white, with a certain predilection for the former -- were raped by Northern troops during the so-called "American Civil War"
(see, for example, WAR CRIMES AGAINST SOUTHERN CIVILIANS by Walter Cisco).
This does not appear to have occurred in Spain, on either side.
Perhaps Machado was correct in this sense, that the Spanish have an innate sense of dignity which is never entirely lost.
C.P.