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How to report bugs in other systems found via their use in SageMath is an excellent question.

One of the aspects is whether it is a bug in the other system, or in the Sage interface to it.

In case of doubt, the best is to report on the Sage side, at Ask Sage, sage-support, or sage-devel. Then others can help determine if the bug is from the other system or from the interface.

For bugs that definitely belong to the other system, ideally one should try to reproduce directly (without using Sage), in order to report them "upstream" (which means to the other system that Sage uses).

If the bug is reported on both sides, it's good to cross-link the bug reports.