The question of understanding the scaling limit of metric graph critical loop soup clusters and its relation to loop soups in the continuum appears to be one of the subtle cases that reveal interesting new scenarios about scaling limits, with a mixture of macroscopic and microscopic randomness. In the present paper, we show that in three dimensions, scaling limits of the metric graph clusters are strictly larger than the clusters of the limiting continuum Brownian loop soup. We actually show that the upper box counting dimension of the latter clusters is strictly smaller than $5/2$, while that of the former is $5/2$.