Not sure what you mean.
Did he forget to make a sight rail (actually a channel)?
Does the kydex snag on the front of the rear sights?
Depending on where and by how much, kydex can be made to forgive some things. Just be sure you have measured accurately, measured again, checked your figures, and most iportantly have some basic idea of what you are going to be asking the kydex to do.
But most importantly of all - why can't you discuss the problem with the guy and have him fix it/redo it?