Multiplayer like lag in singleplayer

I have been experiencing very annoying issues that are identical to those found on a server running slowly such as delayed damage, delayed opening of inventories (chests, hoppers, etc), mobs freezing, sounds stopping, hoppers skipping chests, blocks reappearing and the items not coming out of blocks instantly, etc.
The lag seems to come in short waves every now and again. I have attached a video showing the hopper lag, sound stopping and items not coming out of blocks instantly.

I am not sure how to reproduce this, it has been doing this only on this build and I have restarted my computer. Note: The video is heavily compressed. I'm not sure if the items out of blocks being delayed was very clear.