Here is a C++ source code:

# cat -n test.cpp
 1  #include <memory>
 2  using namespace std;
 3   
 4  int main(int argc, char **argv)
 5  {
 6      auto_ptr<int> x;
 7      auto_ptr<int> y;
 8      auto_ptr<int> z;
 9   
10      return 0;
11  }

Command line to compile it with C++11 standard:
g++-4.7 -std=gnu++11 -Wall -Wextra -Wdeprecated-declarations  -pedantic test.cpp 

Here is the g++ output:
test.cpp: In function ‘int main(int, char**)’:
test.cpp:7:19: warning: ‘auto_ptr’ is deprecated (declared at /usr/include/c++/4.7/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
test.cpp:8:19: warning: ‘auto_ptr’ is deprecated (declared at /usr/include/c++/4.7/backward/auto_ptr.h:87) [-Wdeprecated-declarations]
test.cpp: At global scope:
test.cpp:4:5: warning: unused parameter ‘argc’ [-Wunused-parameter]
test.cpp:4:5: warning: unused parameter ‘argv’ [-Wunused-parameter]

A warning about auto_ptr being deprecated has been issued only for y and z. I expect a warning for x too.

Moreover, if I leave only one auto_ptr (say, x) I will see no deprecation warning at all.

It is expected to see warning on every auto_ptr instantiation.