Hi. I am following a tutorial by Paul Esteves.
This is where I am at the moment:


I want to avoid the pinching I highlighted. I am a bit overwhelmed by the amount of parameters in Houdini. I raised the substeps, but that is not the issue. I wonder if I need to increase the Stretch Stiffness or if the balls aren't dense enough. I am also thinking if the collide needs to have more polygons.

What do you think I could do to make the balls reshape and conform to the box and the other balls without losing their shape to the extent that they completely lose the air when squeezed?

It's hard to say without seeing the file. New users often change parameters that an experienced user might leave at default values. The first thing I would try is changing the resolution of those spheres. Try making them lower res and simulate again. Basically rearranging where the points are on the surface might prevent them from latching onto something.