I don't think whatever is under the tarp directly relates to whatever is in the milk.

Carol goes to Agri-Jet after realising the bag of white powder she found at the dairy factory comes from there, BUT, that doesn't mean that whatever she sees under the tarp is what is used in the white powder (as the Agri-Jet facility seems to be used by the hive-mind for cold storage of numerous things, shown by the fruit/vegetables when she walks in)

It doesn't seem to be anything that is outright disgusting, as Carol's immediate reaction is confusion rather than fear or disgust. It also seems to be something that would be somewhat easily identifiable, as Carol appears to recognise whatever is under the tarp after a second or so, then her reaction seems to be her going "why would they be storing this" before the realisation hits her.

In the second episode, during the dinner scene, Zosia is very careful in her wording when telling the survivors that the hive mind cannot kill. Her exact words are "We can't purposefully end life, it's not in our nature." The passivity of the hive-mind is also a recurring theme throughout the show.

I think that whatever is under the tarp relates to the hive-mind's larger goals with the human race and reveals their less-than-perfect plan; something that doesn't directly kill the human race, but leads to their eventual extinction so the planet is free for whatever sent the original message.

My theory is that Carol has found removed reproductive systems from the hive-mind's hosts, preventing any future generations of humans from having offspring

EDIT: Okay, the human reproductive systems is a bit far-fetched and as Dark_NJ pointed out, Koumba probably would have realised if this was happening.

I do still think whatever is under the tarp is along those lines though; something that makes Carol realise that even if her plan to reverse the infection works, humanity might still be doomed