The code used was from the wiki:
mods.mekanism.Infuser.removeRecipe(minecraft:mossy_cobblestone);

This is because of Infuser.java which uses mekanism.api.infuse.InfusionInput and mekanism.api.infuse.InfusionOutput. This no longer exists.
It seems to have been replaced by RecipeHelper.java. Unfortunately according to the comment, this is going to be removed in the next update. The mekanism wiki page talks about the replacement, IMC based integration.

The sawmill also seems to have had changes as occurs when trying to remove a recipe from the sawmill.
The code used was also from the wiki:
mods.mekanism.Sawmill.removeRecipe(minecraft:fence);

Here is a link to ItemStackInput.java.

Fixed in ModTweaker2 0.9.0. Please update!

Sorry is there any option for a solution coming up? Not sure how I should handle this on the modpack end. Not willing to give any pressure, just would like to get an information about how this could be handled :) thanks!

IMC is not even an option for anything with modtweaker btw. IMC happens too early.

Sorry, I'm not very familiar with forge. It looks like the maintainers will have to talk with the mekanism devs to sort something out then.

possible duplicate of #91
confirmed this bug w/ mekanism 8.1.1.225 MT2-0.7.5 MT3-9.0.9C