Whats the most annoying bug?

[DanW]

Every time a stage separates I have to reselect my target.

So if I have three stages , after each stage separates I have no target selected.   I have to focus on the planet again and choose set as target. 

Next stage goes and repeat again.    Why?

[DrCHIVES]

I actually haven't noticed this one.  I mostly select my targets after reaching orbit and going to build my maneuver node.  I'd have to pay attention to that later when I get on.  

[Periple]

Joints occasionally going out of joint when coming out of warp.

[Scarecrow71]

Parachutes not opening.

[magnemoe]

For me its I say 2 is the node bug, suddenly the burn indicator does not work. Not an huge deal as you can still burn and its done then trajectory overlap the prediction. I often just delete the burn and adjust.
1 is sometimes you can not create nodes as the create node disappears then you try to click create node. If hard to fix just create one, you can warp to an 0 d/v node after all. Even set it up in alarm clock mod, this is how I mark about to reenter in alarm clock. 

[Superfluous J]

Most annoying? Probably the game not remembering what I had focused or which direction my camera was facing with going between map mode and vessel mode.

Not the most troublesome or worst, but for sure it annoys me the most.

[adsii1970]

The time bug. Start the game. Play for a while, look at the clock and realize you’ve been in front of your PC for the last seven hours with very few breaks. 
 

and nothing else got done that day…