Microorganisms have a definite shelf life and they need to be grown on optimum medium for continuous multiplication.
they can grow beyond control sometimes and then become difficult to get rid off.
it is tedious to separate the organisms from the products as they are very small, more so if the sizes of the microbes and the products are very similar
microorganisms are living beings and for no reason at all they can all die or grow abnormally and a new batch of organisms will then have to be procured, getting the same strain would then be difficult
a single base difference in genetically modified microbes used to produce proteins for antibiotics etc will form spirulous proteins. even a shift in the reading frame may lead to this. therefore it is better to use tissue culture for these.
many of the microbes used in such processes are antibiotic resistant and therefore they need to be heat killed before they can be discarded