I create TONS of lanes when I'm working/testing out song ideas and I've never had that happen. Perhaps the project has been corrupted. Have you been using Save As to create versions while you work? Perhaps you can go back to an earlier version.
Another thing I'd look at is all the possible Arm statuses. Maybe you have the record button armed right on one of the lanes which I believe would overwrite despite the current mode (but I never use that button). I'm sure you would notice that but you never know... sometimes simple things get overlooked when we're deep in the thick of things.
If it persists I'd contact Cake. Maybe you found a bug. Good luck.