Stages firing prematurely?

[Jokurr]

So I built this probe that is designed to land on Duna, but first it docks with a space station in LKO, where a booster which has the fuel it needs to reach duna is already docked. The way my design worked out is it has a surplus of fuel by the time it reaches the space station, so I transfer what fuel the ship has onto the station. This stage is then discarded. However, whenever I fire off this stage, all other stages seem to go off as well. It turns on any engines, and also activates my parachutes. Not sure why this happens. I press spacebar once, and it's like it becomes stuck and it fires off all remaining stages. This only seems to happen after I dock with another ship/station.

Is this a bug or am I just doing something wrong here? Is there a way to get around it? I have a mechjeb module on the ship if that has anything to do with it, though I'm doing the docking manually and don't have mechjeb activated when it starts firing stages.

[Noticeably FAT]

Open the ascent guidance window and turn off auto stage.

[astropapi1]

Your staging changes once you dock with another craft. It's better to decouple it manually.

[Jokurr]

Open the ascent guidance window and turn off auto stage.

That seemed to work, thank you! I guess the auto stage likes to do it's thing even when the autopilot isn't enabled.

[NeoMorph]

One of the ways I got around the joint staging problem is to add extra stages and tell MJ to stop at stage 4 or 5. As long at the ship you dock to has less than that it won't auto stage I find.

I do hate it that you can't trigger a stage from the stage icon on the left hand side. Sometimes you need to trigger a certain stage component manually (like when I docked with another vessel and I ended up with the stages mixed up. I wanted to ditch an almost empty tank that I had transferred the fuel from but I had to dig around in the 3D view to try and locate the stack separator under engines and monoprop tanks because if I hit the stage button I would have probably ditched some part of the other craft too. In the end I just undocked, staged and then re-docked. Docking is so simple these days (after lots of practice) that it's no hardship. But newbies would have a lot harder time.

It would be nice to colour code the mixed stages of the various docked ships of the gross vehicle... or tag the stages with a code like Ship1, Ship2, Ship3 etc. How about a line from the stage list part to the 3d rocket that can be turned on and off. All good ideas that a decent coder (which I am not these days) could probably do in their sleep.