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Are you sure that your CMakeLists.txt and package.xml are properly configured? I've tried compiling your code and it went completely fine (using "catkin build" command, ROS Kinetic).

In package.xml you should have "depend" fields for all needed packages.

My CMakeLists:

cmake_minimum_required(VERSION 2.8.3)
project(message_filtering)

find_package(catkin REQUIRED COMPONENTS
  message_filters
  nav_msgs
  roscpp
  sensor_msgs
)


catkin_package(
)

## Build ##

include_directories(
# include
  ${catkin_INCLUDE_DIRS}
)

 add_executable(filtering src/filtering.cpp)

 target_link_libraries(filtering
   ${catkin_LIBRARIES}
 )