After reading through this thread, there are a few rather important questions that remains unanswered.
You have referred to a "separation agreement," but I didn't see any reference to a judgment or decree or order issued by the court. Was your "separation agreement" incorporated by the court into a judgment, decree, or order, or is it just a private agreement between you and your child's other parent?
If the "separation agreement" was incorporated into a judgment, decree, or order, then no, the magistrate does not have the power to disregard it, but it's not clear that's what the magistrate was doing.
You said that the "separation agreement" requires your child's other parent to "submit the bill/receipt for [unreimbursed medical] expense[s] to [you] within 30 days." Ok; that's fine, but it doesn't tell us much. First, "within 30 days" of what? Does it say? If it doesn't say, then it is open to interpretation. It would be unreasonable to interpret it to mean "within 30 days" of the date on which the expense was incurred (which I bet is how you'd like to interpret it) because there may be times where the party incurring the expense won't know if it will get reimbursed (either fully or in part) until after 30 days from the date on which the expense was incurred. The more reasonable interpretation would be to require submission of the bill/receipt "within 30 days" of the date on which the expense was incurred or, if later, the date on which the party incurring the expense learned that the expense would be either fully or partly unreimbursed.
More importantly, what, if anything, does your "separation agreement" say is the consequence of not submitting a bill/receipt "within 30 days"? My guess (and I could, of course, be wrong) is that it says nothing about consequences. If so, then the document was poorly drafted because, again, it leaves the matter open to interpretation, which means that your allegation that the magistrate was "disregard[ing] the terms of [y]our separation agreement" isn't well taken.
My guess is that you'd like to interpret the agreement such that your child's other parent forfeits her right to reimbursement from you if she fails to send you a copy of a bill/receipt "within 30 days." But a court is not going to apply such a harsh interpretation without clear evidence in the language of the agreement that it was the parties' intent that this would be the consequence. Since you have not mentioned anything about a provision in the "separation agreement" that provides for consequences, I have to assume none exists.
So what is the court likely to do? Probably (and this is where case law comes in, but no one on a message board is going to research case law for you), because the law generally abhors forfeitures, the court is going to want you to demonstrate that the other parent's delay cause you prejudice. Let's say that, on January 10, 2011, your child's other parent incurred $100 in medical expenses that she knew on that day would not be covered by insurance. On January 10, 2013, she presents the bills/receipts for those expenses to you. How have you been prejudiced? As an initial matter, you will have to overcome the fact that the delay actually benefits you to some extent. How? Let's pretend that you are able to earn interest of 5% per annum on money that you don't have to spend immediately (of course, that rate of return isn't readily available in this day and age, but it illustrates the point). In this case, you have earned $10 in interest on the $100 you didn't have to spend on January 10, 2011 and, accordingly, have benefited from the other parent's delay.
One possible way of demonstrating prejudice: Let's say your child needs a prescription every month that has a $150 co-pay. It might be fairly easy for you to come up with $75 per month (1/2 of the co-pay). However, coming up with $1,800 (24 months x $75) in one lump sum might present a hardship for you.
Even if you can demonstrate prejudice, it might not result in forfeiture. Taking the prior example about the prescription, the court might simply order you to pay the other parent $75 per month for 24 months. It might present a slight hardship (since you'll be paying your share of the current co-pay plus your share of the former co-pay), but it's a far less significant hardship then coming up with $1,800 in a lump sum.
When the magistrate said "there is no case law to support it," he probably was referring to the general reluctance to find a forfeiture in the absence of clear contractual intent.
I hope this provides you with a helpful framework for dealing with this issue going forward.