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Yes, but it's very rare now a days. I live in JVM land and there are quite a few native JNA libraries that I have run into issues with. One example is vlcj [1] I just ran into yesterday. I have yet to dig deeply into the issue just yet, but it's giving me the fun "no compatible architecture found error". SWT and JavaFX both fully works with arm now though, so I am pretty happy on that front. GraalVM native-image also does not support building ARM on Mac yet either. On the C/C++ side of things I have not ran into any incompatibility issues in the last 5 months. I'd say 99% of my time is smooth sailing at this point.
[1] https://github.com/caprica/vlcj
