This is one of those times when Wikipedia summarizes it quite well, but basically Berle shows the SCTV guys no respect, and Genius Winner Joe Flaherty tries to defer to him but can't help snapping back a bit. Miltie didn't really like sharing the spotlight, did he?
What I wonder is, who made Milton Berle the time police? He and Martha Raye are presenters, not the hosts of the ceremony. I guess he just took it upon himself to try to dismiss the next generation of comedy.
Catherine O'Hara remembers this moment in a 2020 Entertainment Weekly piece reflecting on an Emmy win for Schitt's Creek. The story notes that SCTV responded, in a manner, to the incident with a parody sketch the next season that featured Flaherty pummeling a Berle stand-n and telling him he would never ruin another acceptance speech!