Since your not showing this in a context, it impossible to answer. The norm has a different gradient than the squared norm, and many weird things can probably happen with the non-smooth norm. Additionally, in some cases you might have a problem which is SOCP-representable, which YALMIP automatically will extract from quadratic epressions. If you use sqrt(x'*x) you will get a general nonlinear program even if it would be SOCP represenatable if you had used the norm operator, or squared the expression
If you have a non-convex problem, any minor change can lead to huge differences in solution and solution time.