Add missing stacklevel=2 to 12 warnings.warn() calls (#10260)

Without stacklevel, warnings.warn() reports the location of the warn()
call itself rather than the caller's location, making it harder for
users to identify the actual source of the warning in their code.

This adds stacklevel=2 to all 12 warnings.warn() calls across 10 files
that were missing it.

Co-authored-by: Asif Saif Uddin {"Auvi":"অভি"} <auvipy@gmail.com>