Kerbal Space Program

No, this isn't because there are two nodes, after an encounter is set and no nodes are present a new one can't be created if the two lines are close.

(I can't re-open bug, requesting change to Confirmed)
I would state that this is a bug, with regard to handling how maneuver nodes are added and manipulated to the traces, if said traces are very close to each other (see also #2029)

It appears that nodes tend to prefer the stable trace after an encounter. This is likely because it is calculated after the current trace, so might be higher in the virtual framebuffer (if anyone knows what I mean when I say that).

A possible solution, if it is possible to detect both traces, would be to use a key (maybe Tab) to select between the two when the cursor is near (this is TI's solution on the nSpire handheld). Another solution could be to ask which trace is intended (Scribblenaut's solution for words with multiple meanings), but this isn't as smooth a solution. A third solution, which would accomplish it in a roundabout way, would be to allow one to make the node off the intersection, and then drag it into place without it jumping to the other trace. A fourth could be to prioritise the current trace unless there is a node later on the trace.

No matter the solution used, the problem gets pretty annoying.

Also would like to add this is still present in 0.23, TruePikachu is describing the same problem I did in the OP.

I'm not entirely sure about my surmised internal analyses now, because I might have encountered the bug in a non-overlapping system (I was in Mun's SoI, and couldn't add a point to the internal trace, despite it not being anywhere near the stable trace).

Oddily enough, I only had this happen the one time; earlier today, I was putting nodes all around the Mun without issues, but I couldn't put down a node my last flight. I wasn't able to check what would happen if I would remain in orbit around Mun, however, because of my speed and single ion thruster.

I also have this problem with Version 0.23 on Linux. Often when I enter the SOI of some object, I can not set a maneuver node right away. Sometimes it is possible to set a maneuver node further down the trajectory and drag that node to the desired position, but not always.
This bug should definitely be reopened (and fixed).

I just had this problem in version 0.24.2

I had a very similar issue; I would suggest that in the Mun Orbit training scenario, that the helptext be updated to remind you to remove old maneuver nodes. I managed to forget to remove one and this was the first result on google; removed the extra node, now it works as expected. (Or, maybe have an error when trying to click an orbit when there are too many maneuvers active?)

Still exists in version 0.25.0.

I now use the following work-around:
1) install the precise node mod
2) Put a maneuver on the post-encounter trajectory (near where you actually want it on the pre-encounter trajectory)
3) click the "o" button in the precise node window to access the options and enable "Use x10 UT increment". This enables "-/+ orb" buttons for the maneuver time.
4) click the "-Orb" button. The maneuver is now on the pre-encounter trajectory instead of post-encounter. Success!

I could still reproduce the issue in KSP 0.90.0.705 with the previously attached save.

I still face this. (I have quite few mods in though). Though in most cases it is triggered when I encounter Minmus. Steps:

0. I have MechJeb and few parts mods(B9, KW, NearFuture,...) along with others.
1. enter orbit of Kerbin
2. match planes with minmus
3. Execute Hohmann transfer via node planer - though its a bit modified version( less delta-v so I can perform breaking manuver near Minmus and use its gravity to pull me towards it)
4. wait and look when ship accelerates
- orbit unfolds properly
- cyan orbit disappears and violet one kicks in. It unfolds few times from Periapsis( very fast, sometimes skips unfolding and just gets bigger in jumps)
5. Once ships stop accelerating I get two orbits, now it depends, either I can not add any new maneuver( ever) or I can, when Im able to it gets weird. When I add it, orbit flickers and boom, new node is gone, but not entirely - it appears on new, green orbit(more or less circular, but not tied to Kerbin, out side of its area of influence) somewhere in the outskirts of system.