I know that you can break a truss rod by over-tightening it. Repair guides warn not to tighten the rod if you meet excessive resistance or hear squeaking noises. For example, from the Fender Bass Guitar Setup Guide:
In either case, if you meet excessive resistance when adjusting the truss rod, if your instrument needs constant adjustment, if adjusting the truss rod has no effect on the neck, or if you're simply not comfortable making this type of adjustment yourself, take your instrument to your local Fender Authorized Dealer.
I also know that some guitars require a little neck relief to prevent fret buzzing, so over-tightening a truss rod has aesthetic risks too.
Are there any other significant risks when adjusting a truss rod? I’m especially interested in any long-term problems that a truss rod adjustment could cause, that might not be immediately obvious at the time of adjustment.