Description:
When you design a LV with the main engine and verniers, the verniers could burn for a little bit longer. Therefore, mechjeb considers them as a separate stage, but with the same number as the main engine stage. And, if you want to use this stage as an early shutoff one, mechjeb optimizes the wrong stage - not the main engine, but the verniers.

If you set the min dV setting to 0, you can see this behavior. Moreover, because there's 2 stages with the same number, mechjeb stalls indefinitely.

Now the bug from the title. If you set the option to non-zero, the displayed list looks correct. But, the stage to optimize is still the wrong one! No (optimize) word next to the 6th stage.

So, it filters out only the displayed stages, not the ones available for optimization.

UPD: It looks like this bug appears only if there's an additional stage to burn after the optimized one. If the stage to optimize is the last one, everything seems to be ok

MechJeb version: DEV 2.14.3.0-1412

Steps to reproduce:
Design an Atlas/Thor vehicle and set the early shutoff stage in the settings.

Expected result:
Mechjeb should correctly select a stage for optimization based on the min dV-filtered list.

Actual result:
Mechjeb tries to optimize the incorrect stage.