It's not uncommon, particularly if you use your dump valves to correct buoyancy (which a lot of new divers do). Nothing particularly bad or wrong with it; it's part of the learning process.
As said above, eventually you will reach the point where you correct your buoyancy primarily with breath control. Amazing things start happening then: your BCD will have significantly less water in it, you will consume less air, your hair will become radiant and have more body, your skin and nails will be flawless, you will become popular among certain religious sects who may worship you as their god. Your personal experience may vary.
In seriousness, regardless of whether you have a lot or little water in your BCD, make sure you are rinsing it out thoroughly with fresh water post-dive. I use a little bit of antibacterial detergent (maybe a capful) and water when rinsing; I put the solution in, blow air into the BC and slosh the mixture around the bladder (like shaking an unusual cocktail), empty it out, and then flush several times with fresh water. Hang it upside down in a dry room with air inflator hose disconnected for a couple days.