This was just a matter of need and existing precedent, or lack thereof. Prior to the Mexican-American war, Mexico controlled both Alta California (modern-day California and territories extending eastward) and Baja California, and had a reason to name them differently. After the US annexed Alta California, it had no other portion of California that it needed to disambiguate, and as a result no reason to call the new territory "Upper California" when "California" was already unambiguous. Mexican Baja California simply retained the name it already had.