One limitation is that maintaining sterility over extended periods in continuous culture can be difficult, as can the subsequent processing of cultures due to the continuous nature of the system. Another drawback is the heterogeneity and viscosity of the culture mixture pose difficulties in sustaining filamentous organisms. There's also a risk that a faster-growing strain might outcompete the original product strain over time, potentially resulting in the loss of the desired characteristics of the culture. Lastly, regulating the generation of non-growth-related products can be difficult in continuous culture setups.