There are times, especially in Mountain Biomes, where ones tombstone is not at the location shown on the large map. My son was getting very frustrated, because his tombstone was not at the location shown on his map. I had just ported in and went to help him. After climbing the first hill from our portal tower, I spotted his tombstone right in front of me. He was not even visible to me, when I looked to see how far off he was. Extremely contoured terrain like mountains, can place ones tombstone on the map along way off from where it actually is.

I know this is not always the case, sometimes the game does glitch, but try running in an ever widening spiral if your tombstone is on contoured terrain. There are dev commands to spawn items lost due to game instability in the early access stage. I have had to use it when I lost a Lox Saddle, after placing it on a tamed lox that was glitched.