How do scientists use radioactive dating
These are often characterised as the norm, rather than the exception.
You can't deform a structure (e.g., bedding) that is not there yet!
However, note that because of the "principle of cross-cutting relationships", careful examination of the contact between the cave infill and the surrounding rock will reveal the true relative age relationships, as will the "principle of inclusion" if fragments of the surrounding rock are found within the infill.
Cave deposits also often have distinctive structures of their own (e.g., spelothems like stalactites and stalagmites), so it is not likely that someone could mistake them for a successional sequence of rock units. Each of them is a testable hypothesis about the relationships between rock units and their characteristics.
This orientation is not an assumption, because in virtually all situations, it is also possible to determine the original "way up" in the stratigraphic succession from "way up indicators".
For example, wave ripples have their pointed crests on the "up" side, and more rounded troughs on the "down" side.