Fix rare edge-cases pip crashes

There are some rare edge-cases in the pip code that seem to
be triggered randomly by tests. We had originally thrown
exceptions for these; however, as we head for release-ready,
we can turn these into just logs instead.

Bug: 230321185
Test: various presubmit runs (aggregated over time)
Change-Id: Iea47516fb6f6ccd625493d42a3c2b5236468f602