Yes, that definitely happens. As things freeze, especially large amounts freezing gradually, the pure substance freezes first, eventually concentrating impurities in some other part. Given enough time, it all must freeze, locking impurities ... somewhere. And it is true that a pure crystal isn't always perfect and pure -- things other than water molecules can be part of an ice crystal. This will deform the ice crystal, but that's ok, no crystal is made of absolutely perfect repeating molecular subunits. Otherwise -- think about it -- it would never end and have a surface.