Reproduction steps:

• create a symbolic link to a folder (lets call it LinkToFolder);
• put the attached project folder "Test" on it;
• open the project "Test.pro" on Qt Creator — IMPORTANT: When asked to choose the project file, choose it through LinkToFolder — and configure the default shadow build;
• compile the project. I let a missing semicolon in main.cpp, so a compile error will occur;
• on the "Issues" panel, the first issue message points to main.cpp through the original folder (the one LinkToFolder points to). If you open main.cpp clicking on this issue message, Qt Creator thinks the file is outside the project, which will cause the warning "This file is outside the project directory" when trying to edit it;
• the second issue message points to main.cpp through LinkToFolder, so, opening main.cpp clicking on this message causes no problem.

I could only reproduce this problem using subdirs projects. If you try to open the subproject "sub.pro" directly, this problem will not occur.