That's just a consequence of the small sample size, and consistent with the 95% confidence estimate ( nuci ) you get for nuhat if you use the following commands:
rho = 4.5; nu = 5; N=100;
U = copularnd('t',0.4,5,N);
[rhohat,nuhat,nuci] = copulafit('t',U)
If you use N=1000, you'll see much tighter bounds on nuhat.