I'm relatively new at homebrewing, so take my advice at your own discretion...it sounds like you may have racked to secondary a bit early (sounds like your fermentation wasn't quite complete), but you should still be OK. What kind of activity were you getting in your primary's airlock? I would wait for things to calm down in the secondary, then rack it to another carboy/bucket (to get it off of any yeast cake or trub that might be sitting in the bottom of your secondary) and let it sit for a while (until you get little or no activity in your airlock). Once you're there, you should be good to go for bottling. If anything, the additonal conditioning should help your brew clear up some more and allow more time for your trub to settle to the bottom. As they say, Relax, Don't Worry, Have a Home Brew
Just some advice from your friendly neighborhood noob...if anyone has a better idea or if I'm way off here, feel free to correct me.
-Josh