To put it another way - PIT runs your unit tests against automatically modified versions of your application code. When the application code changes, it should produce different results and cause the unit tests to fail. If a unit test does not fail in this situation, it may indicate an issue with the test suite.
I've seen code that works well for a piece of middleware, but when the stack is complete, testing the entire stack is always done with perfect data.
An entire stack failing due to a piece of the stack for so many reasons is so common.
Testing is a skillset that many don't have without experience.