The particular implementation of an instruction set is probably copyrighted (don't quote me on this), which is why AMD and Intel don't simply copy each other's designs even when one is behind the other (like AMD is now or Intel was back in the Pentium 4 days). There's also the possibility that Apple or another ARM licensee creates their own extensions to the ISA (like AMD did with the basic 32 bit x86 ISA), for which they could indeed get patents.
The term "secure enclave" itself is just a marketing term used to package the particular collection of techniques that Apple uses. I'm not sufficiently familiar with the details to say whether the techniques used by Apple are industry-standard or were invented in-house.
If they are industry standard, others would be using them by now.
Remember Apple co-founded ARM, as one of the original licensees they are not as restricted as others with what they can do.