cleaning gravel

Sounds like you either didn't rinse your gravel properly in the first place OR you have cheap, nasty gravel that is painted / dyed and this colour is leaching off! :(
 
If it is new return it. If old, either keep rinsing, should be non-toxic dye so it is up to you, or get some new. Could be the friction of stirring and rinsing is rubbing the dye off worse than normal.
 
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