This behavior is caused by a setting called "Automatically pretty print in the Sources Panel" which seems to be set as default. In this case, the "wrong" line numbers after pretty-print are actually consistent with those of the minified code.
For example, if you only have 1 line in your minified code, you will only have Line 1, Column xxx after pretty-print.
In short, you can simply turn off Automatically pretty print in the Sources Panel at DevTool Settings --> Experiments --> Automatically pretty print in the Sources Panel
, and reload DevTools.