NaNs indeed can get different bit patterns, but my point was that, given that you need to explicitly bit-reinterpret the NaN to have that affect anything, that can't really affect most code. I guess perhaps blindly hashing a NaNs bits? (that of course goes under your "you weren't handling NaNs […] properly anyway")
For NaNs, if we're being strict then you don't need to reach that far. Here's one example from LLVM:
https://github.com/llvm/llvm-project/issues/43070)
This can occasionally result in visible bugs, like: https://github.com/rust-lang/rust/issues/110174
You have to be pretty nitpicky to care about this stuff and it's not an issue in practice, but it's a reproducibility violation because it deviates from the standard nonetheless.
Those LLVM issues are unrelated afaict - the former is high-level IR optimizations that just result in non-reproducible NaN bit patterns (and the things that wouldn't be just NaN bit patterns I can't even repro on the reported llvm 8.0 or any other version I tested)
The latter though is indeed a proper compiler bug, min/max are an awful mess... didn't know that the ARM fminnm/fmaxnm that were that funky though, caring about sNaN vs qNaN... makes them essentially unusable for compilers (not even useful in known-not-NaN contexts, as then fmin/fmax are equivalent)
NaN handling is ambiguous in two different ways. First, binary operations taking two NaNs are specified to return one of them in IEEE-754. Which one (if they're different) isn't defined and different hardware makes different choices. Second, I'm not aware of any language where NaN propagation has simple and defined semantics in practice. LLVM essentially says "you'll get one of 4 randomly chosen behaviors in each function", for example.