No, not at all.
Whatever their invoice policy, you have done the work and they are liable to pay. There is no way around it.
They might not be happy. They might be entitled to ask for an invoice for their records. That doesn't mean they can just ignore it.
It is very unlikely that your contract said that no money was due if you didn't invoice within a certain period of time and even if it did you would have an argument under UCTA that is an unfair term.
You can always sue them if you need to although obviously that would be damaging to your relationship with them.
Can I clarify anything for you?