First off, my answer will really only focus on Soviet decision-making. I can't really address the Cuban thought process.
As you imply in the question, the Soviet Union and Somalia had close relations from the mid-1960s until 1977, and had signed a treaty of friendship and cooperation in 1974. Given that, and the $300 million in arms given to Somalia between 1974 and 1977^1, it would be easy to assume that the two countries were close allies, and that the Soviet decision not to support Somalia was illogical.
However, Robert Patman identified several Soviet discontents with their Somali allies in that period from 1974-77. They are:
Ideological confusion- Soviet commentators remarked negatively at the failure of Somalia to develop a "vanguard party" along Marxist-Leninist lines. Additionally, they were disappointed in Somalia's incomplete nationalization of the economy, and the continued presence of the private sector in the country.
Statements made by Siad Barre that Islam was one of the realities of African Socialism, saying^2
'In our country religion is not just a matter of faith: it is inherent in our culture and has its own social structure.' And because 'imperialism has always tried to use religion as an instrument against communist ideas, we decided that in our country there should be no struggle between religion and social- ism.'
Aside from the Soviet perception that Islam as practiced in Somalia was incompatible with Socialism, those remarks and other actions raised Soviet fears that Barre was attempting to build closer relations with Gulf States including Saudi Arabia, which were hostile to Soviet influence.
Concerns about "narrow nationalism", i.e. Barre demonstrating Somali national sovereignty by publicly rebuking Soviet influence during the Berbera missile crisis, and expressing openness to friendly relations with the US.
The Soviet perception that Barre was shopping around for aid from Soviet rivals, including China and the Gulf States.
On the other hand, Soviet foreign policy viewed the 1974 revolution in Ethiopia as the shaking off of an "imperialist-feudalist" regime of Haile Selassie, and Ethiopia taking steps forward towards the democratization of the social order and (aspirationally) towards socialism.
In the two years after the revolution, the Derg faced many internal enemies, including secessionist/nationalist movements in Eritrea and Oromia, as well as internal resistance to their land reform program.
In the face of that internal resistance, as well as the ballooning capabilities of the Somali armed forces (supplied by the Soviet Union), the Derg appealed to the United States for military aid. However, the Ford administration only offered a small package of aid, out of a desire to avoid offense to the Gulf States which supported the Eritrean cause. The new Carter administration refused any military support, citing human rights violations by the military regime in carrying out the war against Eritrean rebels.
Therefore, Ethiopia next turned to the Soviet Union for military aid, in 1976, which was granted.
This support for their longtime rivals (the Ethiopians) for their fight against the Eritreans incensed Barre and his regime in Somalia. In fact, Somalia had been quietly providing support for the Eritrean Liberation Front for several years.
Finally, one last factor that influenced Soviet policy against Somalia happened when in March 1977. The Soviet Union and Fidel Castro proposed a confederation of Ethiopia, Djibouti Somalia and South Yemen into a socialist bloc in the Horn of Africa edit- but with only minor changes with respect to national borders, leaving Ogaden an autonomous region in Ethiopia. Barre rejected this proposal outright, and reaffirmed Somali claims on the Ogaden.^3
This was taken as intransigence by the Soviets, reaffirming their fears of narrow Somali nationalism.
This was heavily reliant on the book The Soviet Union in the Horn of Africa by Robert G. Patman.
1- Soviet Union in the Horn of Africa pp 178
2- ibid pp 136
3- ibid pp 202-03
Not cited here, but worth a read is this paper