There are many bug when trying to break/place a block an a plugin cancels that.

Canceled breaking:

• Next to a fence/iron bar/(stained) glass pane: The block is visually no longer connected
• Doors/Double plants/Beds: The other half of the block disappears (similar in 1.12 for double plants/beds) - doors are not bugged when cancelling break, only when cancelling interact
• Double Chests: The broken half is invisible or the other half exists double (2 chests at the same position) - depending on what side you try to break
• Stairs: When placing another stair at the front or back so that they try to connect

Canceled placing:

• Next to a fence/icon bar/(stained) glass pane: The block is now visually connected to a not existing block
• Attaching a chest to another chest: The chest is now invisible
• Stairs: When breaking another stair at the front or back when they are connected

Possible solution: Resend the neighbor blocks to the client if necessary 

Test plugin source: https://pastebin.com/2aNZHauB