I think it will be some more information needed. Because when transaction stuck on some layer there should be exception, error code, log message that is responsible for such behaviour.
If there is non because such functionality is normal for your application but you want to measure it from some different reason it will be hard to help without knowledge about application. You can always try to prepare business transaction that has two filters. First will be method invocation from layer you are talking about and second one has to be negative. For example if there is any method that is executed only when transaction is going to different layer make measure of method invocation on it. That add it to business transaction as negative condition in filter this may work. Remember that all measures that are filter should have Upper Threshold setup to 1.
But as I've said to you it will be hard to help without proper knowledge 🙂
If you want both of them maybe there is single method that always is executed on this layer. Then you should simply prepare BT with single filter on measure Method Invocation with upper severe threshold to 1 and this should be fine.