You can file an appeal, but that requires a substantial bond. If you had an attorney, you should discuss your options with him. If not, you should contact an attorney immediately as there are deadlines to file an appeal.
It is possible to unwind a guilty plea, but the motion is complex. You should contact an attorney to weigh the cost/benefit of doing so. Your son may also be able to apply for a restricted license that will allow him to travel for work or school.
The DMV is a governmental agency with employees that are well known for making mistakes. And the tough part is getting them to correct such errors. It sounds like a mistake was made here. So take all your paperwork to the DMV and see if they will straighten it out. If not, you can file a writ of mandumus in court that will compel the DMV to correct its error.
You should definately contact an attorney. If money is tight, and you don't want to forfeit the amount that the bail bondsman charges, we can likely get him released without bail, or get bail drasstically reduced at the arraignment. The DA might be able to offer a very good deal becasue the facts against him are very weak.