Not sure if this is common, however I have been troubled by this bug for a while.
On any activity using MUP it seemed to fail due to a timeout error, like this:
Meteor Up: Production Quality Meteor Deployments
------------------------------------------------
Started TaskList: Stopping Application (linux)
[111.111.111.111] - Stopping app
events.js:85
throw er; // Unhandled 'error' event
^
Error: Timed out while waiting for handshake
at null._onTimeout (/usr/local/lib/node_modules/mup/node_modules/nodemiral/node_modules/ssh2/lib/client.js:138:17)
at Timer.listOnTimeout (timers.js:110:15)
Anyway, I found the reason in this thread: https://github.com/arunoda/meteor-up/issues/401
If you’re using a custom port (I am) you need to update the setting to use the string ‘port’ not ‘Port’ (lowercase).