PyPy makes tradeoffs that might not be acceptable. For anything that isn't a long running server, PyPy can be much, much slower since the JIT doesn't have a chance to warm up. PyPy also implements things differently: repeated string concatenation in a loop is quadratic instead of linear like in CPython. There's also memory tradeoffs, depending on what you're doing.

The list of differences is quite long, and even though most of them are edge cases, it's not hard to get bitten by one on a project of any substantial size:

https://doc.pypy.org/cpython_differences.html

It's not that people are writing weird code, it's that you have a package that does something clever but safe, and then another package using it that calls it in a way that's unexpected but not documented as unsafe, and layers and layers of that compound until you have things like exceptions raised because non-string keys are getting set on type objects.

At the end of the day, Python isn't a terribly well-specified language. CPython behavior is functionally the specification. "Make it match CPython but faster" isn't really an option because it kills your ability to do a lot of the things that make PyPy fast. And if that was all it took, we wouldn't still be arguing over a JIT inside CPython. Pyston was an honest attempt at doing that, but it has been dead for years partially because it hit many of these walls.