Could you send me the input file that gives you this problem? The atoms of the reactant and product must exactly correspond, and my experience is that sometimes this is not how they are initially and sometimes it is not trivial to get them that way. Maybe if I look at it I can help.

I think you didn't get same number to all atoms in two molecules , go to gaussview and use connection Editor

That's what I mean - the molecules have to be aligned and the atoms numbered identically - be sure that's the case - but sometimes that's not how it is first done by the Connection Editor or even by the "Enable Autofixing" button in Connection Editor. So swap the numbers on the atoms so that they are the same on both molecules. Then try the QST2 again. But like I said, send me your input molecules and I'll see if I can help.