In 2000, Milano and Doherty were filming the third season of "Charmed" when they stopped speaking to each other and Milano threatened to quit if Doherty wasn't fired.
I don't think anyone is really sure what happened between the two of them. There are rumors and theories but it might just come down to them not getting along and both of them not wanting to share the attention. Doherty left the show before producers had to address Milano's demands.
They never did learn to play well with each and still don't get along today.