Why was saint Stephen canonized? I know that you have to perform three miracles to be canonized, but I don't know what his were.
Veneration of martyrs (such as Saint Stephen) as Saints among the Christian faithful long predated the formal process (to include miracles) which later became a standard and evolved into canonization. Martyrs were prominent among the early saints venerated by Christians.
Among other things, persecution sparked the devotion of the saints, facilitated the rapid growth and spread of Christianity, prompted defenses and explanations of Christianity (the "apologies") and, in its aftermath, raised fundamental questions about the nature of the church.
Put a different way, you have asked an anachronistic question. There was no formal requirement for having performed three miracles when Stephen was recognized as a saint. (credit to @bruisedreed, for how to say that concisely).
The formal process of canonization never really stated until the 10th century, when Pope John XV declared that for a beatification a miracle was needed and had to be approved by Rome and two additional miracles were needed for a canonization.
Before this time, canonizations were investigated at the diocesan level by the local bishop (6th-10 centuries).
Moreover in the Early Church (1st-5th centuries), canonizations were generally proclaimed by the People of God (Vox Populi, Vox Dei). This is how St. Stephen was proclaimed a saint and in these times no miracles for sainthood were required.
In the first five centuries of the Church, the process for recognizing a saint was based on public acclaim or the vox populi, vox Dei (voice of the people, voice of God). There was no formal canonical process as understood by today's standards. Beginning in the sixth century and continuing into the twelfth century, the intervention of the local bishop was required before someone could be canonized. The intervention of the local bishop usually began with a request from the local community for the bishop to recognize someone a saint. Upon studying the request and a written biography, if he found it favorable, the bishop would typically issue a decree, legitimatize the liturgical cult and thereby canonize the person.
Starting in the tenth century, a cause proceeded with the usual steps, i.e. the person's reputation would spread, a request to the local bishop from the people to declare the person a saint occurred, and a biography would be written for the bishop's review. Now however, the bishop would collect eyewitness testimony of those who knew the person and who had witnessed miracles, and he would provide a summary of the case to the Pope for his approval. The Pope then reviewed the cause, and if he approved it, he issued a decree declaring the person a canonized saint. The first documented case of papal invention is by Pope John XV on January 31, 993 for the canonization of St. Ulric. When Pope Sixtus V reorganized the Roman Curia in 1588 he established the Congregation for Sacred Rites. One of its functions was to assist the Pope with reviewing causes. Except for a few canonical developments, from 1588 the process of canonization remained the same until 1917 when a universal Code of Canon Law was promulgated.
The 1917 code contained 145 canons (cc. 1999- 2144) on causes of canonization, and mandated that an episcopal process and an apostolic process be conducted. The episcopal process consisted of the local bishop verifying the reputation of the person, ensuring that a biography existed, collecting eye witness testimony and the person's written works. All of this was then forwarded to the Congregation for Sacred Rites. The apostolic process consisted of reviewing the evidence submitted, collecting more evidence, studying the cause, investigating any alleged miracles and ultimately forwarding the cause to the Pope for his approval. This process remained in effect until 1983 with the promulgation of the 1983 Code of Canon Law and new norms for causes of canonization: Divinus Perfectionis Magister, Normae Servandae in Inquisitionibus ab Episcopis Faciendis in Causis Sanctorum and Sanctorum Mater (2007). This revised process for causes of canonization is still in force. - Saints