Hello and thanks for this game 
I think there is a bug with agglomerator, cause when I use it, sometimes one of the effects disappears. I tried to make a drug which need catalyst, and each time agglomerator remove this one from used ingredient with it. I don’t have this problem if I use plenty of evaporators or some Cryogenic Condensor.
I tried to change its position from ingredient with Shaker, but same issue.
Have you checked if the effect is on the remove condition?
Say´s the remove condition is between 12-15 and can be removed with an Agglomerator.
If yes then you need evaporators to get beyond the remove Condition.
This is probably the remove condition on the side effect that has the catalyst. If so, it’s not a bug and you should just use 3 evaporators (or a higher level machine) instead.
I think not, but I’m not sure, looking now 