Water inside your BCD *does* affect bouyancy in two ways... but if it's a just a little bit there's nothing to worry about...
1) Since it's the same weight as the water, you loose displacement and therefore bouyancy... if it didn't matter, a BCD wouldn't need to hold any air for you to control your bouyancy. While a small amount won't have a *major* affect on your bouyancy, a BCD that won't hold air or otherwise inflate isn't going to do anything for you.
2) Since water is denser (heavier) than air, it'll go to the bottom of your BC. If it is a significant amount (eg. 2# of water), then your trim will be affected and you might have a hard time staying horizontal, level or whatever position you're trying to maintain. Basically you have 2 extra lbs that you're trying to hold in a position it doesn't want to be held at...
As for what it means and what to do about it... if it's a lot of water, and you have problems with bouyancy (eg. constantly added air or letting air out even at depth) it can mean you have too much weight in your weight belt...
What to do about it... drain it as best you can after you dive, right there at beach or boat... if you're going to dive within the next day or so, you don't need to do anything beyond that... if you're done for the week or whatever, then rinse the inside out... add a good bit of water... stick the inflator up to a hose or faucet... add a gallon or so... swish it around... drain it... repeat until it's not salty... yes, taste the water draining out... if you couldn't drink it... it's not clean yet... when it's fresh water again... drain the best you can... inflate... leave sitting so the lowest part is your inflator... then drain again in the morning after all the water collects at bottom overnite...
Big reason you do the rinse thing is because of the salt crystal forming and cutting the bladder inside the BCD... oh and last thing is be careful of heavily clorinated water like pools... it's not quite as bad as salt water (eg. crystals) but it's not like fresh fresh water either... if you do pool diving... think about using a BCD conditioner every so often.
Dave