I created a mechanical crafter setup to auto-craft cakes on a server. A while after I had finished up with it, I noticed that it had stopped crafting (it had successfully made 300 cakes by this point). The problem appeared to be that the 6 buckets i had in circulation in the system had disappeared. In trying to figure out what went wrong, I discovered that:

• The mechanical crafter was no longer working: the cake recipe would go through the crafting animation before failing, with all items dropping to the ground.
• Breaking the mechanical crafter blocks caused a server crash.
• After the crash, 6 of the 9 blocks seemingly disappeared instead of dropping in item form.
• Subsequently placing and breaking any mechanical crafter blocks in the same spaces the previous ones occupied causes a server crash.
  I don't really know what I'm talking about but my guess is that the 6/9 crafter blocks which disappeared after being broken somehow got the buckets stuck in their inventories and are still present in some ghost block form.
  I could certainly do more testing on the issue but I'm not very keen on it since every crash entails waiting a few minutes for the server to restart, and more importantly there are other people playing on the server.
  Also my apologies if a similar issue has already been posted, I browsed through open issues but didn't spot one.

This issue has been marked as stale because it has been inactive for 3 weeks. It will be closed if it remains inactive for another 3 weeks.

This issue has been closed since it has been inactive for 3 weeks since it was marked as stale.

Found a Similar, if not the same issue.
I Created a mechanical crafter setup to auto-craft tnt on a server. Made TNT once to test if it's working, And then connected pipes to it (Mekanism Logistical) (Valhelsia 3 Modpack). The materials were piped in correctly, but I decided to destroy and move the Mechanical crafter somewhere else - Destroying it with a pickaxe.

Mid-way Destroying it, the server i've been playing on, Crashed.
When I re-joined the server:

• 5 out of the 9 crafter blocks were missing.
• The Mechanical Crafters that had gunpowder in them, When Destroyed, Crashed the server again.

Everything seems to be matching what lucayde has said on the issue.

I Can similarly try testing it more - But again, as my predecessor, I would rather not crash the server, making others wait a few minutes each time for it to restart, and Probably causing frequent roll-backs.

The Common point between me and my predecessor seems to be that there were remaining items in the mechanical Crafters - wether they were intended to be there, or Not.