I can't reproduce:

$ clazy-standalone rule-of-three/main.cpp -checks=rule-of-three  -- -Wno-unused-value -Qunused-arguments -std=c++14 -isystem /data/installation/qt/x86_64-5.9/include -fPIC 

4 warnings

With -I instead of -isystem there's 13 warnings

Maybe you have some other -I

reopen if you have a test-case, I can't repro

Did you try with relative path in -isystem like in my example?

Yeah, also works with relative:

$ clazy-standalone rule-of-three/main.cpp -checks=rule-of-three  -- -Wno-unused-value -Qunused-arguments -std=c++14 -isystem ../../../installation/qt/x86_64-5.9/include -fPIC 
In file included from /data/sources/clazy/tests/rule-of-three/main.cpp:1:
/data/sources/clazy/tests/rule-of-three/main.h:5:1: warning: HasDtor has dtor but not copy-ctor, copy-assignment [-Wclazy-rule-of-three]
struct HasDtor // Warning
^
/data/sources/clazy/tests/rule-of-three/main.h:10:1: warning: HasDtorAndCopyCtor has dtor, copy-ctor but not copy-assignment [-Wclazy-rule-of-three]
struct HasDtorAndCopyCtor // Warning
^
/data/sources/clazy/tests/rule-of-three/main.h:27:1: warning: HasCopyCtor has copy-ctor but not dtor, copy-assignment [-Wclazy-rule-of-three]
struct HasCopyCtor // Warning
^
3 warnings generated.