Each effect is neutralized in almost in all cases by the same weapon it comes from. In the case of the raining magma, blow it up with ShouenZan or Magma Blade. For iced floors, use Hyoroga/Ice Burst. For gnats, use Yammark Option. For iron blocks, use Metal Anchor/Rakukojin. For soul spirits, use Laser Shield. Finally, red crates can be blown up with SentsuiZan/Ground Dash; black and blue ones can be moved with the same weapon. The rain and the spotlights cannot be neutralized.

Amazon Area, Laser Institute: Metallic gnats (very pesky)
Amazon Area, Magma Area: Metallic gnats
Inami Temple, Amazon Area: Normal rain (slows you down)
Inami Temple, Central Museum: Normal rain
Magma Area, North Pole Area: Magma rain. Also, some walls break an allow access to secret area.
Magma Area, Weapon Center: Magma rain.
Weapon Center, Amazon Area: Spotlights (dispiriting and very difficult to maneuver with)
Weapon Center, Inami Temple: Spotlights
Laser Institute, North Pole Area: Soul spirits (attacking soul clones of Zero/X, respectively)
Laser Institute, Inami Temple: Soul spirits
North Pole Area, Recycle Lab: Iced floors
Recycle Lab, Magma Area: Iron blocks
Recycle Lab, Weapon Center: Iron blocks
Recycle Lab, Central Museum: Iron blocks
Central Museum, Recycle Lab: Red, blue and black crates
Central Museum, Laser Institute: Red, blue and black crates