Each aliquot of peptide is deposited into each vial via machine. The vial is then stoppered and moved inside the lyophilizer. Once in the lyophilizer, the vial is then given a nitrogen flush to rid any contaminates. This is the phase that will determine the appearance of the contents.
Sometimes the water vapor can escape the vial where it goes from a solid to a gas without every going through a liquid phase. This will make the contents adhere to the sides of the vial leaving very little to see by the naked eye. Other times, depending on several other factors including temperature, the appearance can look like a solid puck, a few smaller pucks, a powder material, or even just a few specks, but the amount of actual material is the same.
When freeze drying products without any matrix (sucrose or mannitol for example) sometimes the residual water of hydration will cause a collapse via hydration of product before it fully dries. In other words, when the water from the ice crystals is removed what remains prior to secondary drying (when the chamber is warmed) can combine and solubilise the remaining material causing it to collapse. Sometimes it forms crystals and sometimes it forms films dependent upon how much there is local melting and what the temperature and vacuum levels are at the time of the collapse.
Very complicated but it tends to happen far less when sucrose for example is around since the sugar hydrogen bonds to the protein/peptide like the water did and thus less water remains bound as water of hydration