It seems that your samples were thawed during the lyophilization. It can happen if the sample is large or the vacuum is not enough. I suggest freezing small volume samples at - 80 C.
Hi Subin, it sounds like your protein was moistened, probably for poor vacuum....or alternatively the sample has high salt concentrations and absorbed moisture
The isopropanol that is used in the buffer is indispensable. I am isolating the protein fraction based on its solubility i.e. solubility in alcohols like isopropanol.
Check how clean all components (including isopropanol) are on drying, one may not dry down well. Often sugars are used with proteins being lyophilized, but without solvents proteins are not sticky. Did you get rid of lipids? They partition with isopropanol.