In the end no manufacturer can make a “full proof” aircraft and it is up to the pilots to know each aircraft’s “quirks” and systems to fly it properly and safely.
It even is OK for any aircraft to have some "quirks" and it is OK not to redesign if you discover them, as long as the overall accident statistics are fine and the change would even add more confusion to those used to the "quirks". It is quite typical to use some flying techniques which are not exactly textbook style because of design peculiarities, the "Boeing push" comes to mind for example.
The only important point is that you acknowledge that some points of your design might be a bit special or tricky, and include them in detail in the handbooks and in the training syllabus. If pilots are fully aware and trained accordingly, any design feature can be safe. If pilots are poorly informed and trained, even simple and straightforward design features might be a major risk. An airplane alone is never "wrong", only in combination with the pilot training it may be.