In my experience with compilers where phase ordering causes fires, it's exactly to do with the IR.
Because I don't want to pick on others (as much fun as that would be), I'll just pick on compilers I wrote that have this property and how much I regret everything I did there.
- The first compiler IR I designed was called Fiji C1, and it had both an SSA form and a not-SSA form, and it had multiple stages of lowering within the same IR. You absolutely could not breathe on the phase order without destroying everything.
- I'm maybe like mostly responsible for JavaScriptCore's DFG IR, which has a LoadStore form, a ThreadedCPS form, and an SSA form, plus maybe other forms too. And there are many phases in there that serve the purpose of carefully lowering some aspect of type speculation. Foolish is the man who tries to mess with the order of those phases.
- The Assembly IR in JavaScriptCore's top tier JIT has different laws before and after regalloc, and before and after stack alloc. That's maybe inevitable and like not too bad since it also has a small number of phases, but still.
Note that in each of these cases, it absolutely is an IR issue. It's not like there were some rules that I failed to follow. It's that I designed the compiler specifically to have an IR that follows different laws in different parts of the pipeline.