Out of hundreds of chars only on my newest one did i go though the trouble of getting dogmeat from the scrapyard since i plan to get the puppies perk at level 22, but to avoid him getting killed until then i had him wait in my Megaton house (yes i know the puppies perk will still work even if dogmeat died before the perk was taken).

It took until level 10 for me to get to the Water of Life quest since i did a couple of side quests before hand but during the part in the quest when you have to escort Li and the others though the tunnel and have two enclave troops on a catwalk that you have to walk under about half way though the tunnel section i told Li and the others to wait in the hallway so they would'nt get in my way, but after killing both of the troops i went back to the hallway and found dogmeat waiting by the door as if he was told to wait there and Li was in the other room.

Another odd thing that happened was when i reached the part where you find BOS troops in the tunnels and get ambushed by a bunch of ghouls, instead of running to a safe place Li ran straight at the ghouls and started punching them and then went to a corner to cower in fear after they were all dead.

I'm not really looking for a fix for the problem or an explanation but mainly just warning others about the problem so they can somewhat expect it to happen.