Okay, this is pretty simple to reproduce. I created a Drying Rack from Artisan Valley (But you can use any custom machine):

• Click on a custom machine in the crafting menu to craft it
• Instead of clicking on an inventory slot to place it there, click somewhere outside of the window to throw it instead
• Pick up the custom machine you just threw
• The game will crash

Crafting a machine, putting it in a slot, then placing it down and breaking it and picking it up does not crash the game. However, this method does crash, no matter which custom machine you use (it does not do this for regularly crafted items). I'm using SMAPI 3.0 & Stardew 1.4.

SMAPI-crash.txt