I siliconed my legacy and my kickside with red RTV about two weeks ago and as I was throwing them the silicone slipped out and the bearing shredded it to pieces. Any tips? Am I doing something that would cause this?
Probably nothing you did. Silicone falls out, its no big deal.
Silicone falls out. It is supposed to happen. Now you have 2 options: You can buy replacement pads (here:http://shop.yoyoexpert.com/product/56/YYJ-Silicone) or you can
re-silicone them again yourself. Personally, I use “permtex red HI TEMP silicone.” You can buy this stuff at any hardware store. It looks like this… http://img2.prosperent.com/images/250x250/www.outdoorpros.com/images/prod/1/Permatex_81160.jpg.I’ve found through experince, this stuff works the best, and lasts the longest. Hope this helped. 
P.S. The original pads probably fell out because you got some lube in them, which causes them to expand out of the yoyo. So in the future, avoid getting lube all over the silicone pads.