Hi,
the alignment process is iterative. So if you don’t clear the RC cache, the next alignment will take previously aligned components into consideration to create new components.
If your alignment is creating too many components than it might indicate image overlap problems or bad RC alignment settings.
I’d recommend to take a look at this information: https://support.capturingreality.com/hc/en-us/articles/115001528211-Taking-pictures-for-photogrammetry