Orphan sections are sections present in the input files which are not explicitly placed into the output file by the linker script. The linker will still copy these sections into the output file by either finding, or creating a suitable output section in which to place the orphaned input section.
If the name of an orphaned input section exactly matches the name of an existing output section, then the orphaned input section will be placed at the end of that output section.
If there is no output section with a matching name then new output sections will be created. Each new output section will have the same name as the orphan section placed within it. If there are multiple orphan sections with the same name, these will all be combined into one new output section.
If new output sections are created to hold orphaned input sections, then the linker must decide where to place these new output sections in relation to existing output sections. On most modern targets, the linker attempts to place orphan sections after sections of the same attribute, such as code vs data, loadable vs non-loadable, etc. If no sections with matching attributes are found, or your target lacks this support, the orphan section is placed at the end of the file.
The command-line options --orphan-handling and --unique (see Command-line Options) can be used to control which output sections an orphan is placed in.