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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}
)