Added warning flags for usages of MPS

[jlarson4]

Description

Added warnings when using MPS by default, to ensure users are aware of potential computational anomalies that may occur. This should resolve #1178

• New feature (non-breaking change which adds functionality)

Checklist:

• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• I have not rewritten tests relating to key interfaces which would affect backward compatibility