Who knows. This has been up for debate for years and it looks like Midway is never going to explain. There's two theories.

1. In an attempt to get Scorpion to kill Sub-Zero Quan Chi lied to Scorpion and told him that Sub-Zero had killed his family and clan.

2. Scorpion's MK II and UMK3 endings were non canon and he had been after Sub-Zero the whole time.

So there's no real answer? Well that sucks. Maybe they just forgot about it.

There's no real answer. People insist their view is right but Midway has never been clear either way. Take your pick I guess. I personally believe Chi fooled Scorpion but whatever.

Shaolin Monks seems to ignore the whole thing completely, so either Midway forgot or just doesn't care.

He tries to kill Sub-Zero because Quan Chi brought Scorpion back to life. Scorpion remembered having a wife and kid, Quan Chi told him Sub-Zero killed them, and Scorpion got pissed.

Scorpion's MK4/G bio states that Quan Chi PROMISED to bring him back to life to gain him as an ally in the war against the Elder Gods. It doesn't say that he did that.

Nor does he say he's after Sub-Zero again....

That's where his ending comes in, his "alterior motive", but even then, we're never told why he decides to go after Sub-Zero again when he wasn't during MK3.

well for one thing Sub-Zero's clan and the former clan that Scorpion was in were enemies. really i think it was just Quan Chi manipulating Scorpion to do his dirty work for him to take out the Lin Kuei (for what reasons? i dunno). im not sure if this is true but i remember some one saying that Quan Chi told Scorpion that it was actually the younger brother that killed his family and clan. so he went out after Sub-Zero for revenge, and as Scorpion was about to kill Subby, Quan Chi was stupid enuff to say that he fooled Scorpion into killing Sub-Zero, but he said that b4 he did kill him.... stupid Chi...

anyways it maybe not 100% confirmed exactly what is up with this issue, but what ive said in t his post makes the most sense atleast.