Okay, this is the kind of bug I expect to see quite a lot of - adding and removing modules is tricky, when you delete a module it’s supposed to inform all connected modules that it’s being removed - so they can clean-up and unplug cables and reset their state… if a module doesn’t do that correctly when you come to reconnect it it thinks the sockets are still populated even though there’s no visible cable. I’ll havde a look at a patch with clocks, switches and dividers and try and replicate.
It’s an easy fix once I’ve found where it’s happening! If it does happen it’s pretty unrecoverable, you can try deleting the module with the issue and then add a fresh version of it.