The Phantom Nether glitch (from 1.12 or below) isn't patched.
HOW TO REPRODUCE:
Go to Nether, enter this command "/setblock ~ ~ ~ minecraft:nether_portal
Try to explode TNT, it won't work unless you go in survival but dropped items are in a loop in creative.

EDIT: Found this in the log "Can't keep up! Is the server overloaded? Running 33829152ms or 676583 ticks behind", that's a very large number.