Respiratory systems. The further from the outmost membrane (the larger and “deeper” an organism), the more time and energy require to diffuse oxygen throughout said organism. If an organism is nearly two dimensional, theoretically this wouldn’t be a constraint at all: oxygen and carbon dioxide could diffuse freely and easily without any required effort from the organism (i.e breathing cause by internal pressure fluctuations).

There’d be a point in a three dimensional organism where the amount of effort required to carry oxygen throughout the entire body is too much to justify its size, placing a size constraint on the organism. To my understanding, this scales with atmospheric oxygen in insects, which is why earth used to have quite literally giant insects. The more atmospheric oxygen, the larger life as a whole can grow. Definitely speaking a little out of ignorance here, so feel free to correct me if I have the wrong impression.