1) Complexity of Design: One of the biggest drawback of hybrid topology is its design. Its not easy to design this type of architecture and its a tough job for designers. Configuration and installation process needs to be very efficient.
2) Costly Hub: The hubs used to connect two distinct networks, are very expensive. These hubs are different from usual hubs as they need to be intelligent enough to work with different architectures and should be function even if a part of network is down.
3) Costly Infrastructure: As hybrid architectures are usually larger in scale, they require a lot of cables, cooling systems, sophisticate network devices, etc.