You know it's a pretty common thing for horses to be afraid of. All my babies went through this. I've had retrained miniatures, TBs as well as full sized drafts to be sprayed and washed down with water hoses, so I've dealt with all sorts of horses.
Keep the spray bottle during groomings. Because we don't know for sure what scares her(could be the bottle, could be the sensation of the spray, could be the color, could be the sound of spraying); keep the bottle on your belt or in your hand during your grooming sessions.
From there(days or a couple weeks later, whenever she is settling with the idea), from a distance spray the brush you are going to be brushing her with then brush her. Do that for a little while longer.
Continue on with slow re-introducing spraying her directly again. Stay away from her face and head, start off with the main parts of her body. Make sure you let her know she is being a really good girl with it.
Let us know if you have problems with hosing her down. Another very common issue with babies. I'll be more than happy to advise with that as well.
Take it slow with them and be very patient and they will get it.