Can cooking in a larger than intended vessel be disadvantageous in some way?
Every pressure cooker has a minimum amount of liquid which it must be filled with, in order for that liquid to evaporate and provide the pressure increase.

Check the manual for your pressure cooker to ensure that the small quantity of lentils you want to cook is at least the minimum.

If it is not, you can either prepare more lentils (hopefully you can use the leftovers), or perhaps get a smaller pressure cooker.

Of course, it doesn't take very long to cook lentils conventionally, so when you want only a small amount, you might consider cooking it in one of the traditional stove top or oven methods.