I have rebuilt my sugarcane collector multiple times because of the issue, and got tired of it
So, I have built sugarcane collector inside minecart and left it to go forth and back, stopping it on powered rail when storage is full (Also removed the cart assembler, so minecart was working restless)
SOMETIMES when I'm leaving home chunks to travel, the contraption disappears and the only thing left is minecart.
Also happens on re-joining world, sometimes contraption stays here and sometimes it disappears, leaving lonely minecart.
My assumption here is that data about structure isn't always saved to minecart when chunk is getting saved/unloaded and thus said data gets lost.
Anyways, further investigation required, I've seen it happening while playing on server and unfortunately didn't test in in singleplayer yet.

Mod version: 0.2.2b (the latest one)
Forge version: 28.2.0

I am having the same issue.
It started happening out of the blue, I am not inside the spawnchunks and it worked fine for the last 2 weeks. I moved the "farm" once and now it keeps disappearing.
I am also on multiplayer and when i check the console i get the following message:

[Server thread/WARN] [minecraft/Chunk]: Wrong location! (-15, 0) should be (-15, 1), ContraptionEntity['entity.create.contraption'/186, l='CreateLive', x=-237.00, y=72.06, z=15.99]
[Server thread/WARN] [minecraft/TrackedEntity]: Fetching packet for removed entity ContraptionEntity['entity.create.contraption'/186, l='CreateLive', x=-237.00, y=72.06, z=15.99]

Mod Version: 0.2.2b
Forge Version: 28.2.4

This issue has been addressed in 0.2.3. Thanks for the report and feel free to re-open if need be.