It depends on the cytokine types. There are some cytokines stored into cells in form of precursor (e.g. IL-1 and TNF-alpha). IL-1beta and TNFalpha precursors undergo myristoylation on lysines, which is thought to contribute to their membrane localization. Other cytokines are synthesized and released instantly. Thus, you could have discrepancy in detecting cytokines from supernatant or cell lysate samples, especially if you are observing cytokine levels upon short-term stimulation.