Floaters are unfortunately all too common. The key to determining the source of the floaters is to see where they are on the slide in relation to the tissue. If they are in the same plane of focus as the tissue sample, then they most likely were a contaminate in the block (from either grossing or embedding).
External contamination (eg, water baths or within the staining reagents) typically will show floaters either above the tissue or out of the tissue plane.
Either way, maintaining clean grossing/embedding areas, using a clean water bath, and frequently changed or filtering reagents are the best means of avoiding floaters.
