Leaving your child in the care of others (even those with years of experience) can be stressful on all involved.  The initial first few days require adjustments on the part of all of the players - your son, the teacher and you.  It can take several days or even weeks for everyone involved to learn the expectations and to mesh as a team.  
You mentioned that this is only his second classroom experience.  Unfortunately, 4 year olds, need to rehearse many times before the correct behavior becomes automatic.  During the next few days, be sure to review the rules and behavioral expectations for preschool with your son.  
For instance, based on the example you gave in your post, it would be best to review with your son the rules regarding restroom use.  Break the rules down into simple steps that will be easy for him to remember.  Also, be sure to find out if there are specific times when a child can use the facilities and how the teacher would like a child to gain permission.  In addition, most schools maintain a strict policy regarding adult assistance to children during restroom breaks so you will also want to teach appropriate self care skills. Keep in mind that you can do some things to set your child up for a greater chance for success.  Make certain that your son is wearing simple clothing that he able to maintain himself.  For instance, he should only be wearing a belt if he can manage to fasten it himself.  The same goes for the closure on his trousers or shorts.  Try to find easy off and on clothing that will allow him to use the restroom all on his own.  This will not only keep the staff free to supervise/manage the entire group but will also foster your son's independence.  Greater independence will serve your son well in all settings and ensure success in Kindergarten.
I imagine that arriving to find your son in such disarray was quite unnerving.  Be sure to talk with the teacher about what you observed and how the situation made you feel.  Maintaining yourself professionally will set the tone, hopefully encouraging the teacher to respond in a like manner.  
Remember that the first few days will be an adjustment period.  If you find that you still have concerns regarding the teacher's expectations, her professionsalism or her ability to see the good in your son's behavior after the first week or so, you should schedule an appointment to discuss your concerns more directly.  Best wishes to you and your son!
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