What is your best example of this?
Personally, my best example is in Tears of the Kingdom. Linearality was never a problem but there was one funny moment where it messed things up for me. I was randomly exploring and I tried to get up to an area in the thunderhead because I got a shrine ping. I got the shrine, and then I explored a bit before being thrust into a main quest for a sage. After completing it and doing more things in the game, I do a main quest which was actually supposed to get rid of the thunderhead and then get there safely, and THEN do the sage quest I ended up accidentally doing. It was annoying but really satisfying.
Personally, my best example is in Tears of the Kingdom. Linearality was never a problem but there was one funny moment where it messed things up for me. I was randomly exploring and I tried to get up to an area in the thunderhead because I got a shrine ping. I got the shrine, and then I explored a bit before being thrust into a main quest for a sage. After completing it and doing more things in the game, I do a main quest which was actually supposed to get rid of the thunderhead and then get there safely, and THEN do the sage quest I ended up accidentally doing. It was annoying but really satisfying.