update: I figured it out. It has something to do with the where the uploads are being stored. I noticed that the very main site that creates the subnetworks stores their uploads in the uploads folder like so
wp-content/uploads
/2016
/bb-plugin
-/cache
-/icons
Then, below all this is the sites folder.
/sites
-/1
–/2016
–/bb-plugin
—/cache
—/icons
-/2
…etc
However, keep in mind that the /sites/1 folder actually still represents the very top network folder (there’s 2 and it’s confusing).
All I did was copy the icons from the main network folder located directly under “uploads/bb-plugin/icons” into the sites/1 and sites/2.
It looks like bb is looking in the /sites directory and was being thrown off by the weird directory structure of a mutlinetwork.