You're quite wrong:
What was held by the Karabakh Armenians until last year was a region consisting of two parts. The former Nagorno-Karabakh Autonomous Oblast and a region which is de jure part of Azerbaijan.
While the remainder of the Nagorno-Karabakh Autonomous Oblast is indeed internationally recognized as part of Azerbaijan, it is not in fact part of Azerbaijan. Azerbaijan seceded from the Soviet Union in accordance with the Soviet secession law. This law can be found on the homepage of Michigan State University, here:https://soviethistory.msu.edu/1991-2/shevarnadze-resigns/she...
The law is from April 3, 1990 and the relevant part is article 3 which reads as follows:
``Article 3. In a Union republic which includes within its structure autonomous republics, autonomous oblasts, or autonomous okrugs, the referendum is held separately for each autonomous formation. The people of autonomous republics and autonomous formations retain the right to decide independently the question of remaining within the USSR or within the seceding Union republic, and also to raise the question of their own state-legal status.´´
That is, for the Nagorno-Karabakh Autonomous Oblast to secede with Azerbaijan there'd have to be a vote in the Nagorno-Karabakh Autonomous Oblast and the 'join the Azerbaijani SSR in seceding' option would have to win. Otherwise the Nagorno-Karabakh Autonomous Oblast would remain in the Soviet Union, or raise the question of its own secession.
The Nagorno-Karabakh Autonomous Oblast became independent only with the final dissolution of the USSR. Azerbaijan's invasion of the NKAO was at first the invasion of the Soviet Union and then later on, an invasion of the now unrecognized successor state-ification of the Nagorno-Karabakh Autonomous Oblast. In their attack on the Soviet NKAO and later the statified, independent NKAO Azerbaijan then lost, to the degree that parts that are de jure part of Azerbaijan were occupied the Karabakh Armenians. These parts were indeed retaken by Azerbaijan, but parts of the NKAO were also taken, and Azerbaijan's claim to these is invalid.
Furthermore, with regard to the Wikipedia article you link, it contains the line:
en "a large column of residents, accompanied by a few dozen retreating fighters, fled the city as it fell to Armenian forces. It is reported that as they approached the border with Azerbaijan, they came across an Armenian military post and were cruelly fired upon".
Such an attack, as described-- i.e. firing on a mixed column advancing on an outpost is permissible according to the laws of war. Thus the so-called Khojaly Massacre, while regrettable, was perfectly legal. This is presumably why Azerbaijan has not pursued the Khojaly Massacre as a war crime in international courts, despite its important role in its internal historiography. Indeed,