If they have deposited the check, but it has not yet cleared, they are likely to be charged a fee by their bank. A prompt phone call to try to prevent that from happening is called for, at least, though it may already be too late.
Also, stopping payment on a check after receiving some consideration for the funds (in this case, having the seat held) could be construed as fraud, or at least breach of contract. Probably the school won't push the issue, but depending on how bored their lawyers are, it may not be, as other posters have said, that the school has no recourse at all for this.