In addition to two reasons mentioned by Alex R. above (columns of $U$, $V$ may be permuted following permutations of distinct singular values $\sigma_i$ on diagonal of $\Sigma$, and permutations caused by equal singular values) there is a third reason connected with the orthogonal complement, too.
Namely, suppose $A$ is a $m \times n$ matrix (assume $m \ge n$). Then the singular value decomposition $A = U \Sigma V^T$ is found from the orthogonal decomposition $A=Q D Q^T$ of the positive semi-definite matrix $S=A^T A$ as by the following steps:
- We take $V=Q$.
- Set $\Sigma$ by adding to $\sqrt D$ some $m - n$ extra zero rows.
- If the first $r$ singular values of $\Sigma$ are non-zero, then we define the first $r$ columns $u_1 \ldots, u_r$ of $U$ to be equal to the first $r$ columns of $AV$ divided by the values $\sigma_1 , \ldots, \sigma_r$ respectively.
- Then the remaining $m - r$ columns of $U$ can be chosen to be arbitrary $m - r$ orthonormal vectors from the orthogonal complement $span^\perp(u_1 \ldots, u_r)$ of the subspace spanned by $u_1 \ldots, u_r$.
So we have plenty of options to choose those $m - r$ columns of $U$ (infinitely many in most cases).