The pistons in the vertical block conveyor are not well-timed causing the block to be pushed horizontally occasionally causing the farm to break. This did not happen in my test server with vanilla redstone implementation. The following attachments are the conveyor in my mangrove farm which I built in my SMP server.

To replicate this bug, try the farm in the world download at a server with alternate-current redstone implementation.

The Mangrove Farm (w/ world download): https://youtu.be/9aWn-DMolxQ

The Vertical Block Conveyor: https://youtu.be/fm36BxDXId8

I've released a new beta for 1.8.0 that adds a new feature to resolve this issue. Changing the update order to vertical_first_outward or vertical_first_inward will make this smart piston design work. Let me know if you encounter issues with this beta or if new problems pop up.

The smart piston on the left in the second and third screenshots unfortunately does not work at all with Alternate Current, but it is also locational, so it should be avoided anyway. Replace it with
this design to fix that issue.

I will consider changing AC's update order to make that design work, but changing the update order will have other effects, so I will have to be careful with that. For example, this 0-tick gen does work reliably with AC, but fixing the smart piston will break it. I will weigh the options and make a decision.

Please let me know if replacing the smart piston in the conveyor works for you, otherwise we'll have to do some more debugging!