Auto-fill is invaluable in the new Industrial Revolution burner phase. Two compatibility issues right now are:
- Doesn't work with IR modded turrets and ammo in at least some cases, and
- Prefers to burn wooden fencing instead of coal.

Is there an easy way to fix this?

Couple of questions, as I'm having trouble reproducing the exact issues:
- Which turrets? I was unable to reproduce this with any of their turrets, and it doesn't seem like they do any auto-replace with turrets when being placed that might confuse the system.
- What is wood fencing? Closest thing I can see in IR is "wood-beam."

That said, I have started working on an update for Fill4Me to allow you to list the current order of fuels and exclude certain ones (as a couple of commands).

Actually you're right. It works for me now, not sure if Deadlock fixed something or I just didn't have the right ammo.

The items we want to exclude from fuel by default are wood-beam and wooden stockades (not surebthe name, it's in military tab), for starters. Those are both useful items you don't want to burn unless absolutely necessary. There might be others I haven't found yet.

Version 0.7.0 adds the commands /f4m.exclude and /f4m.include so that you can /f4m.exclude wood-beam to prevent you from inserting wood-beams anymore. You may find /f4m.list_fuel (and /f4m.list_all_fuel) useful in managing your list of insertable fuels. Please note that the exclude/include lists are per-player; so everyone will need to do that.

Cool! I'll give it a try.

Would you consider adding a remote interface (or some other method) for other mods to add things to a global exclude list? Then IR could call it to exclude any items it wants.

I don't see why not. I'd be surprised if the developer of IR (or other mods) would care, though. I'd have to change the way the exclude list works, since it's not a global thing at current (and an external mod like IR would need it to be global). Order of operations comes into play here too.

Version 0.7.0 adds the commands /f4m.exclude and /f4m.include so that you can /f4m.exclude wood-beam to prevent you from inserting wood-beams anymore. You may find /f4m.list_fuel (and /f4m.list_all_fuel) useful in managing your list of insertable fuels. Please note that the exclude/include lists are per-player; so everyone will need to do that.

Where is this list as its not inserting fuel for me and have it set to insert 10 fuel, but thats on the map settings on the mod settings, don't have anything in the per player settings for fuel in the mod settings, just about ammo

The /f4m commands have to be run in the console (chat window opened by pressing tilde~). It's a prototype feature so not in the actual mod settings yet.