Hello GDarch,
Staff is aware of this visual glitch. It can be frustrating, however, it's possible to keep track of the weather that is currently set. When a Pokemon with a weather setting ability (like Sand Stream or Drought) is switched into battle, the battle text will state this. For example, bringing Pelipper onto the field will result in text that says it started to rain. This occurs if it isn't already raining. These weather effects last for 5 turns unless a damp, smooth, heat, or icy rock is equipped on the pokemon with a weather setting ability. In these cases, the effects last for 8 turns.
By keeping track of when it was first stated that the weather changed and counting turns, you can remain aware of what the current conditions are.
I hope this helps. Good luck pvping and have a great day.