It is well known that Pakistan hosted many anti-Soviet Sunni fundamentalist groups, who continue to generate problems for Pakistan (and the world) to this day.
If Iran did provide sanctuary to anti-Soviet Afghan factions, they most likely would have come from Afghanistan's Shiite minority refugees. On the other hand, I suspect Iran would have maintained a hands off policy in this conflict in light of its war with Iraq at the time.
Iran called for a Soviet withdrawal and aided Afghan Shiites. In the second phase, after the Soviet Army withdrew, Iran helped the non-Pushtun ethnic groups form a united front.
The short answer is yes. To quote from on an article you may want to look at:
The essence of Iran's policy toward Afghanistan was to create an "ideological sphere of influence" by mobilizing and energizing the Afghan Shi'ites, which comprised about 20% of the population, while barely dealing with the Communist government of Afghanistan. Tehran's Shi'i-centered and parochial policy transformed the historically oppressed and marginalized Hazaras, Qizilbash, and Farsiwans Shi'ites into a disciplined and cohesive force. Tehran provided financial support to the Shi'ites, gave them hope, trained a generation of activists, and established close links with the Afghan 'ulama'. The presence of Afghan refugees in Iran provided Tehran with a unique opportunity to train an indigenous Afghan force that was to be relocated to Afghanistan at the opportune moment... Iran's investments paid off when the eight Iran-based Afghan-Shi'i groups formed an alliance in June of 1987.
This resulting "alliance" of Shia mujahadeen was known as the Tehran Eight and formally dissolved in 1989.
