I'm not sure if you're understanding the situation.
When I say the mini machines are created "dynamically", I mean that there a are a set of functions which check what mods are installed, and which machines to create mini versions of, and what the properties of that machine should be (crafting speed, recipe, etc)
Unlike most other mods, I can't set these properties statically (by simply defining them outright) because that might be incorrect for certain sets of mods.
This mod has no hard dependencies (excluding the Factorio Standard Library, which does not itself add any machines). Because of the dynamic way the machines are created, it can work with no other mods, or with many other mods, and the properties would be properly balanced either way, without having to manually define these properties for every single set of mods.
The downside to this approach, is that certain mods can make changes to the base machines that break my mod's logic. For this situation, I can tell there's an issue with how I handle mini-refineries, but I don't know what steps in my functions lead to that end result.
Either a reference is mistakenly being made, or an entity isn't being created, for some reason. If I know what changes are being made to the base refineries, then I can check what steps in the function are being taken (or being skipped).
And again, if I can't reproduce the error, then any changes I make won't be guaranteed to fix it. I'll just be taking shots in the dark that may or may not fix the issue.