Suppose your project structure is the following
MyProject/
├── Rules.mk
├── iproj.json
├── QRPGLESRC/
│ ├── Rules.mk
│ └── hello.rpgle
├── QTEMP/
│ ├── Rules.mk
| └── QRPGLESRC/
| └── hello2.rpgle
| └── Rules.mk
If you try to build QTEMP/QRPGLESRC using either makei b --subdir QTEMP/QRPGLESRC or makei c --files QTEMP/QRPGLESRC (specifying the absolute path also does not fix it), the contents of ./QRPGLESRC get build instead.