Replace some `AssertionError` with other exceptions

[LucaMarconato]

As @jeffquinn-msk observed, assertions are ignored when the code runs in production. We should verify that no assertion is actually required for the logic of the execution, and in case they are required, replace them with other types of exception. Many assertions are used for mypy, but I see some of them are required for a correct execution, so better to look for them and replace them.