Yes I've seen it and have experienced, lots of times. You must have the tubes bend with the bow of the boat. Even just sliding them in a straight tube, up under the gunnels will do that to them.
The main problem it does is just scratch off the clear coating on the rod in certain places, especially where you have high spots like raised ferrules or guide wrapped spots. Your rod will not break at those spots where you see the blank, it's only taking the clear coating off and really just makes the rod look used and worn. Where you have problems with rod breakage is smacking with a fly while casting or doing stupid things like high-sticking a fish, smacking the gunnel with it, smacking the poling platform with it, slamming in the car door, etc... I've seen it all.
I've considered putting some sort of interior reversed sox (made out of some material that would be easy to slide rod guides without hanging it up or scratching the blank) in the tube, because I can get to the end of the tubes in my skiff in the front anchor hatch, to tie wrap that over the end. But can't figure out how to attach it to the front bulkhead side unless I attach a ring with screws where it sits over the rod tube hole, to clamp the sock to the outside edge and then just trim off the sock around the outside of the ring. But the one thing that can't happen is have a fly, hook or lure go in the tube with your rod guides, or you'd be screwed trying to get the rod back out of the holder.
Or maybe gluing the end of some sort of rubber or rubber foam or vinyl sleeve up in the tubes.
I'm in the process of re-doing my skiff and will be doing something like that. So I'll report back to what I ended up doing to solve that problem. I've been thinking about doing it for the last 20yrs and have never gotten around to doing it. But it will get done and done right, even if I have to re-do the tubes to get it right.