Hmm... Sensor tech is something our Starfleet heroes supposedly excel in, as opposed to their brutish opponents. Nevertheless, we have seen Kirk and Picard's teams struggle with locating one of their own inside the Enterprise
, let alone with reliably tracking an intruder. I'd say TOS has every excuse not to feature capturing of intruders by intraship beaming; TNG is on shakier ground, but the nuTOSMovie realm still isn't obligated to be capable of anything of this sort.
Intruder alerts might be largely based on detecting penetration rather than presence, and if the means of penetration is innovative enough, it will go unnoticed. Quite possibly, countermeasures or even detection mechanisms for transwarp beaming will not be invented until several decades into this new timeline...