yeah, I had the same, when I first stated playing with axoloti.
its natural , I think, to follow the wires... and think this is going to be how it works, so i think most of us have been caught out at some time or another. (even if you know!)
i think the axoloti approach is actually simpler than some other graphic languages, but its main disadvantage is (as you pointed out) if your not careful, its easy to break patches by tidying them up.
i think the other reasons it causes problems is many patches will work, even though the execution order is not quite right, because it often doesn't matter if the object is executed on the next cycle. so like anything, if you 'get away with it' most of the time, its easy to get in to bad habits....
i do find though, if you think about execution order when your making the patch its not too bad (easier than fixing large patches later), and it tends to make you do it for every patch...
well, thats in theory what I attempt to do, though I often dont... I guess due to laziness
we do want at some point to give more visual feedback in the patcher, so its clearer to the user what order things are being done... but so many things to do at the moment.