clang-include-fixer--insert-line has an off-by-one error because it uses (goto-char (point-min)) (forward-char chars), which is (goto-char (1+ chars)). Because of this, when the first difference was on an empty line (i.e. an include was appended to the block of includes), the pointer in the to` buffer would be on the next line.
Also wrapped calls inside another process sentinel inside with-local-quit.