Are you using the latest version of samtools and HTSlib? IYes

Please specify the steps taken to generate the issue, the command you are running and the relevant output.

When running samtools coverage on a non-sorted BAM or SAM, while a short error line is printed, the command also prints out a coverage table. The error can be interpreted as a warning given that the program seems to execute correctly. The program should not print a coverage table and instead either only print the error, or additionally print a "You must sort " error. This led me to think my mapping was failing for a long while before realizing sortedness was a requirement. Especially since this requirement is also not noted in the docs.