I'm seeing a bug with Mechjeb 2.11 in KSP 1.11 where adding certain parts in the VAB causes them to disappear from the craft, but the part they are attached to acts like it still has a part attached to it.
Steps to replicate:
1. Start a new craft in the VAB.
2. Add a Mk1 Command Pod
3. Add a 1.25m heat shield.
4. Add an FL-T200 fuel tank.
At that point the tank will disappear but the heat shield will act like it's still attached.
Not sure if this is a known issue or not, but I couldn't find it on the Github issues list. I tested this on a stock 1.11 install with just Mechjeb2 2.11.0 manually installed, in Science game mode.
I have a video of this in action here:
