[Jason Brown] “although I’d be curious as to the reason for this issue for future reference.”
the Extrude tool will only add caps if ‘Create Caps’ is checked and your screen grab shows that it is not checked so the only thing I can think of is that you have duplicate geometry occupying the same physical space (which is possible to accidentally create particularly for a beginner). Try the tool on a new object just to test (disk, sphere etc make it editable select a few polygons and extrude). It should work easily so something odd like duplicate geometry must be going on with your record.
[Jason Brown] “it bypasses the geometry line and selects more polygons than I want, how do I fix this?”
further suspicion that you have duplicate geometry, it should not do that with the tool settings you have in the image.