That error isn't caused by a version mis-match... but you may run into some problems down the road. You might want to switch to petalinux 2015.4. We have a plan to update the ZYBO petalinux project to 2016.2, but no timeframe yet. I wouldn't recommend waiting for it.
Back to the error you are getting, it is probably caused by the fact that your design doesn't have an axi_dynclk core in it, and therefore the system-top.dts file included with the project is trying to modify a device tree node that isn't being created by the tools. I recommend starting with the linux_bd project found in the ZYBO repository on our github, and then making your desired modifications to that project and importing that .hdf. That will ensure that several key aspects of the hardware design we used to generate the ZYBO petalinux project are present in your block diagram. For example, that project also routes an I2C controller over EMIO to the onboard EEPROM so that u-boot can read the globally unique MAC address from it and automatically configure the Ethernet controller to use it. If your design doesn't also route the I2C controller in this fashion, u-boot might fail (as it is configured in our petalinux project), or at the very least, you won't have a globally unique MAC address when you boot into Linux.
Edit: If you want to stick with your project as is and try to get it working, then you will just need to tackle these problems as they come up, and we can help with that. To solve this problem, just open up system-top.dts and remove the node that references axi_dynclk_0 and all other nodes that refer to video output (one will be called xilinx_drm). Note your system will not include HDMI output capabilities.