Stuff floating around in the tank when you do a gravel vac is pretty normal. Your filter should clear it up pretty quickly. To keep the good bacteria at a high enough count to keep your tank cycled, when you clean your filter, if it's a sponge, just squeeze it out in old tank water. If it's one of those floss filters that have carbon inside them, just shake them well in that old tank water, and don't throw them away until the water flow is clogged and they won't clean anymore, or they fall apart.
